A Likelihood Framework for Modeling Pairwise Beta Diversity Patterns Based on the Tradeoff Between Colonization and Extinction

Metacommunity theory and its constituent theory of island biogeography (TIB) have the potential to unify ecology across different scales. The TIB has been successful in predicting alpha diversity patterns, such as species-area relationships and species-abundance distributions, but lags behind in predicting spatial beta diversity patterns. In this study we use island biogeography theory as the starting point to integrate spatial beta diversity patterns into metacommunity theory. We first derive theoretical predictions for the expected beta diversity patterns under the classic MacArthur and Wilson framework, where all species have equal colonization and extinction rates. We then test these predictions for the avian community composition of 42 islands (and 93 species) in Thousand Island Lake, China. Our theoretical results corroborate that longer distance and smaller area lead to higher beta diversity and further reveal that pairwise beta diversity is independent of the size of the mainland species pool. We also find that for the partitioned pairwise beta diversity components, the turnover component increases with the ratio of extinction rates and colonization rates, while the nestedness component is a unimodal function of the ratio of extinction rates and colonization rates. For the empirical island system, we find that beta diversity patterns better distinguish a species-equivalent model from a species-nonequivalent model than alpha diversity patterns. Our findings suggest that beta diversity patterns provide a powerful tool in detecting nonneutral processes, and our model has the potential to incorporate more biological realism in future analyses.

Groups of lakes can be considered archipelagos, and island biogeographic theory can be used to explain the distribution of aquatics within them. Two species of duckweed, Lemma minor and Lemna tremex, were studied as examples. Both are found in southern Ontario, but L. minor occurs much more frequently than L. trisulca. It is this difference the experiments were designed to explain. Colonization capability of each species was defined as its ability to: (1) withstand desiccation, (2) quickly populate a new habitat, and (3) inhibit the other species competitively. Lemna minor was clearly fat superior to L. trisulca in abilities (1) and (2), and in (3) it was judged superior or equal to L. trisulca. Wherever L. minor and L. trisulca are still colonizing recently deglaciated habitats, superior colonization capability alone can explain the more frequent occurrence of L. minor. Southern Ontario lakes may already have reached equilibrium, where the rate of species colonization is balanced by the rate of species extinction. Increases in summer pH above 8 occur, and as both species die above this point, pH could be the major cause of mortality. The observed frequencies of occurrence could therefore be the result of a balance between different rates of colonization and approximately equal rates of extinction.

Island Facts and Theories

Droughts typically result in a widespread decline in many vertebrate populations and even the local extinction of some species. However, different species vary considerably in their resistance to the effects of drought. This study aimed to estimate the relative species richness and the colonization and extinction rates in a bird community during an acute drought event in the Brazilian Caatinga. We mist-netted birds during 3 years throughout seven field seasons in two sampling plots to estimate community parameters using multi-season dynamic occupancy models. The relative richness to the regional species pool varied considerably during the study period (16–49%) with markedly low values in the severe onset of the drought. The estimates in the savanna were higher than those in the shrubby-woodland plot (~ 42 vs ~ 31 species, respectively). Pollinators and seed dispersers were characterized by median to high colonization (30–69%) and local extinction rates (37–69%), indicating low site fidelity. By contrast, granivores and insectivores made up the resident component of the community, with low local extinction and colonization rates (< 30%). Our results indicate that the diversity of Caatinga bird assemblages may decline markedly during severe droughts, primarily as a result of the displacement of species that exploit resources whose availability decreases drastically in abnormally dry years. Considering the climate scenarios predicted for tropical arid and semiarid regions worldwide, we believe that pollinators and seed dispersers will be especially vulnerable to population decline and local extinctions, which will alter community structure and the persistence of ecosystem services.

Habitat fragmentation is one of the most important threats to biodiversity. Decreasing patch size may lead to a reduction in the size of populations and to an increased extinction risk of remnant populations. Furthermore, colonization rates may be reduced in isolated patches. To investigate the effects of isolation and patch size on extinction and colonization rates of plant species, calcareous grasslands at three sites in the Swiss Jura Mountains were experimentally fragmented into patches of 0.25, 2.25, and 20.25 m2 by frequent mowing of the surrounding area from 1993 to 1999. Species richness in the fragment plots and adjacent control plots of the same sizes was recorded during these 7 years. In agreement with the theory of island biogeography, colonization rate was reduced by 30% in fragments versus non-isolated controls, and extinction increased in small versus large plots. Habitat specialists, in contrast to generalists, were less likely to invade fragments. In the last 4 years of the experiment, extinction rates tended to be higher in fragment than in control plots at two of the three sites. Despite reduced colonization rates and a tendency of increased extinction rates in fragments, fragmented plots had only marginally fewer species than control plots after 7 years. Hence, rates were a more sensitive measure for community change than changes in species richness per se. From a conservation point of view, the detected reduced colonization rates are particularly problematic in small fragments, which are more likely to suffer from high extinction rates in the long run.

In this paper, we modify dynamic occupancy models developed for detection-nondetection data to allow for the dependence of local vital rates on neighborhood occupancy, where neighborhood is defined very flexibly. Such dependence of occupancy dynamics on the status of a relevant neighborhood is pervasive, yet frequently ignored. Our framework permits joint inference about the importance of neighborhood effects and habitat covariates in determining colonization and extinction rates. Our specific motivation is the recent expansion of the Barred Owl (Strix varia) in western Oregon, USA, over the period 1990-2010. Because the focal period was one of dramatic range expansion and local population increase, the use of models that incorporate regional occupancy (sources of colonists) as determinants of dynamic rate parameters is especially appropriate. We began our analysis of 21 years of Barred Owl presence/nondetection data in the Tyee Density Study Area (TDSA) by testing a suite of six models that varied only in the covariates included in the modeling of detection probability. We then tested whether models that used regional occupancy as a covariate for colonization and extinction outperformed models with constant or year-specific colonization or extinction rates. Finally we tested whether habitat covariates improved the AIC of our models, focusing on which habitat covariates performed best, and whether the signs of habitat effects are consistent with a priori hypotheses. We conclude that all covariates used to model detection probability lead to improved AIC, that regional occupancy influences colonization and extinction rates, and that habitat plays an important role in determining extinction and colonization rates. As occupancy increases from low levels toward equilibrium, colonization increases and extinction decreases, presumably because there are more and more dispersing juveniles. While both rates are affected, colonization increases more than extinction decreases. Colonization is higher and extinction is lower in survey polygons with more riparian forest. The effects of riparian forest on extinction rates are greater than on colonization rates. Model results have implications for management of the invading Barred Owl, both through habitat alteration and removal.

Estimates of species' vital rates and an understanding of the factors affecting those parameters over time and space can provide crucial information for management and conservation. We used mark–recapture, reproductive output, and territory occupancy data collected during 1985–2013 to evaluate population processes of Northern Spotted Owls (Strix occidentalis caurina) in 11 study areas in Washington, Oregon, and northern California, USA. We estimated apparent survival, fecundity, recruitment, rate of population change, and local extinction and colonization rates, and investigated relationships between these parameters and the amount of suitable habitat, local and regional variation in meteorological conditions, and competition with Barred Owls (Strix varia). Data were analyzed for each area separately and in a meta-analysis of all areas combined, following a strict protocol for data collection, preparation, and analysis. We used mixed effects linear models for analyses of fecundity, Cormack-Jolly-...

We report the extinction and colonization rates of five sympatric small mammal species at a semiarid locality in north central Chile. We provide information based on 6 years of monitoring on how colonization and extinction rates change according to landscape features (slope aspect) and on their relationship to populations size, population variability, and body size. We found that: (1) for all species in the assemblage, extinction rates of subpopulations from equatorial-facing slopes were significantly lower than those in polar-facing slopes, (2) population size was the most important factor determining extinction rates, (3) colonization rates did not vary between slopes, and were affected by population size only in equatorial-facing slopes, and (4) most species had higher extinction than colonization rates. Persistence of the metapopulation system for all five small mammal species appears to be fueled by repeated colonization events.

Effects of climate, species interactions, and dispersal on decadal colonization and extinction rates of Iberian tree species

The theory of island biogeography (TIB) predicts that species richness in isolated areas is determined by the processes of colonization and extinction, and, in turn, governed by island size and isolation. Metacommunity models extend the TIB, predicting that both habitat and species interactions are important drivers of community vital rates and structure, and that marine metacommunities will exhibit higher extinction/colonization rates relative to terrestrial ecosystems. Here we demonstrate that oceanic banks can be considered islands, and document how application of these theories advanced our understanding of the dynamics of these submarine islands following the fishery-induced collapse of predatory groundfish populations. We employed a 48 yr dataset of fish communities on 10 offshore banks of the Scotian Shelf, Northwest Atlantic Ocean to examine colonization and extinction rates before and after the collapse. Bank-specific colonization, extinction and turnover rates were quantified using the island R package to correct for imperfect detectability, inherent to all sampling of natural systems. Colonization and extinction events were briefly unbalanced following the predator collapse, and reflected in increases in species richness and turnover, most notably on the largest banks. However, over the longer term, a dynamic equilibrium of colonization and extinction events prevailed on 8 of the 10 banks. This resulted in a generally time-invariant species richness, and a negative relationship between species turnover and bank area, as predicted by theory. Our study provides support for the relevance of island biogeography and metacommunity theories in guiding exploration and understanding of the mechanisms governing marine community vital rates and structure.

Studying the attributes of biotic communities is integral to all courses in ecology and yet few communities are small enough, or available for effective examination, when classes begin in the fall. Communities discussed in textbooks are usually large and complex, leaving students with the view that detailed studies are difficult and all but impossible. However, it is common for ecologists to partition large and complex communities into smaller, more manageable units called Component communities are usually of sufficient size that all the players can be identified and studied. Component communities are of an ideal size for students to study within the confines of a laboratory period. One type of component community is the insects associated with a particular species of plant. Finding plants with an associated assemblage of insects is easy in most habitats; however, many of these insects are no longer present when students undertake their first field exercises in the fall. Gall inducers comprise one guild of plant-feeding insects still present in the fall and are ideal for studying community attributes. Galls represent one of the most complex insect-plant relationships in the natural world where, by some as yet poorly understood means, these specialized insects redirect the growth of attacked plant tissues and stimulate them into surrounding the larvae with highly nutritious cells and protective tissues. The resulting species-specific structures sustain the insects throughout the summer and shelter them from the elements and predators (Shorthouse & Rohfritsch 1992). Galls are commonly seen by students on field trips and make ideal subjects for explaining the complexities of insect-plant relationships and component communities. Large numbers of galls can be collected within the space of an hour and then returned to the lab or classroom for dissection or rearing. Each species of gall-inducing insect is responsible for a structurally distinct type of gall, making it easy to determine the number of insects present at a site without actually observing the insects themselves. We have found galls induced by cynipid wasps of the genus Diplolepis ideal for exercises in community ecology. Here we describe a simple field exercise that allows students to use cynipid galls for learning about community attributes and biogeography. Diplolepis wasps are restricted to inducing galls on wild roses. Galls are initiated in the spring when tiny adults (5 to 7 mm in length; see photographs in Shorthouse 1993) exit galls from the previous season and lay their eggs in leaf buds or at the tips of stems or sucker shoots. Galls start growing soon after the eggs hatch and immature larvae start feeding. Some galls have a single larva while those induced by other species have numerous larvae per gall. Diplolepis wasps have one generation per year and overwinter in the larval stage inside their galls. There are about 32 species of Diplolepis in North America with each species inducing a structurally distinct gall. Diplolepis larvae are attacked by numerous species of parasitoids (specialized parasitic wasps that complete growth on only a single host) throughout the summer season and the galls themselves are attacked and modified by inquiline cynipid wasps of the genus Periclistus. The assemblage of Diplolepis wasps, parasitoids and inquilines that emerge from a large collection of galls induced by the same species comprises a very distinct component community. Wild roses are common shrubs over much of North America. They are found throughout the northern U.S., Alaska and southern Canada, but some species and associated galls can be found as far south as Arizona or even Florida. They usually grow in patches of varying size and usually have reasonably sharp boundaries. Roses are ephemeral shrubs that frequently become established in disturbed habitats such as abandoned agricultural fields or recently burned land. Single rose plants grow into large patches through vegetative growth and as the years pass, they become colonized by various insects. If roses become shaded by trees and the patches disappear, their host-specific component communities disappear as well. Patches of rose can be considered islands and their colonization by Diplolepis is akin to the colonization of oceanic islands. The strong positive relationship between area and species diversity is one of the few rules in ecology. Demonstrations of island effects are legion, extending far beyond oceanic islands to include any discrete, colonizable habitat such as mountain tops, woodlots (Diamond & May 1981), and clusters of plants of the same species (Janzen 1968). This phenomenon is variously explained as a reflection of increasing habitat diversity as a function of area (Williamson 1981), or as a balance between rates of colonization and local extinction (MacArthur R.G. Lalonde is a Professor of Biology at Okanagan University College, Kelowna, B. C., V1V 1V7, Canada. J.D. Shorthouse is a Professor of Entomology in the Department of Biology, Laurentian University, Sudbury, Ontario, P3E 2C6, Canada.

Declines in grassland diversity in response to nutrient addition are a general consequence of global change. This decline in species richness may be driven by multiple underlying processes operating at different time‐scales. Nutrient addition can reduce diversity by enhancing the rate of local extinction via competitive exclusion, or by reducing the rate of colonization by constraining the pool of species able to colonize under new conditions. Partitioning net change into extinction and colonization rates will better delineate the long‐term effect of global change in grasslands. We synthesized changes in richness in response to experimental fertilization with nitrogen, phosphorus and potassium with micronutrients across 30 grasslands. We quantified changes in local richness, colonization, and extinction over 8–10 years of nutrient addition, and compared these rates against control conditions to isolate the effect of nutrient addition from background dynamics. Total richness at steady state in the control plots was the sum of equal, relatively high rates of local colonization and extinction. On aggregate, 30%–35% of initial species were lost and the same proportion of new species were gained at least once over a decade. Absolute turnover increased with site‐level richness but was proportionately greater at lower‐richness sites relative to starting richness. Loss of total richness with nutrient addition, especially N in combination with P or K, was driven by enhanced rates of extinction with a smaller contribution from reduced colonization. Enhanced extinction and reduced colonization were disproportionately among native species, perennials, and forbs. Reduced colonization plateaued after the first few (&lt;5) years after nutrient addition, while enhanced extinction continued throughout the first decade. Synthesis . Our results indicate a high rate of colonizations and extinctions underlying the richness of ambient communities and that nutrient enhancement drives overall declines in diversity primarily by exclusion of previously established species. Moreover, enhanced extinction continues over long time‐scales, suggesting continuous, long‐term community responses and a need for long‐term study to fully realize the extinction impact of increased nutrients on grassland composition.

Interacting populations in heterogeneous environments

Summary1. A critical need in conservation biology is to determine which species are most vulnerable to extinction. Freshwater mussels (Bivalvia: Unionacea) are one of the most imperilled faunal groups globally. Freshwater mussel larvae are ectoparasites on fish and depend on the movement of their hosts to maintain connectivity among local populations in a metapopulation.2. I calculated local colonisation and extinction rates for 16 mussel species from 14 local populations in the Red River drainage of Oklahoma and Texas, U.S. I used general linear models and AIC comparisons to determine which mussel life history traits best predicted local colonisation and extinction rates.3. Traits related to larval dispersal ability (host infection mode, whether a mussel species was a host generalist or specialist) were the best predictors of local colonisation.4. Traits related to local population size (regional abundance, time spent brooding) were the best predictors of local extinction. The group of fish species used as hosts by mussels also predicted local extinction and was probably related to habitat fragmentation and host dispersal abilities.5. Overall, local extinction rates exceeded local colonisation rates, indicating that local populations are becoming increasingly isolated and suffering an ‘extinction debt’. This study demonstrates that analysis of species traits can be used to predict local colonisation and extinction patterns and provide insight into the long‐term persistence of populations.

1 A number of generalizations have been made as to the effects of the area of occupancy, population size, dispersal ability and body size of species on their relative rates of local colonization and extinction. 2 Here, data on the breeding bird assemblage of Britain are used to test these generalizations. The complete geographical ranges of British birds have been censused twice, in the periods 1968–72 and 1988–91, allowing rates of colonization and extinction between these periods to be estimated. 3 The local colonization dynamics of species are influenced independently by their range sizes and the dispersal abilities of adult birds: species with smaller range sizes and larger dispersal distances were more likely to have colonized new areas between the two census periods. 4 The local extinction dynamics of species are influenced independently by their population sizes and body masses: species with smaller population sizes and body sizes were more likely to have gone extinct from areas inhabited in the first census period. 5 These results remain when controlling for the effects of phylogenetic relatedness. 6 These analyses uphold many commonly held generalizations about the correlates of local colonization and extinction, and suggest that the long-term evolutionary history of these bird species has influenced their potential to respond to current ecological conditions.