Habitat loss, resource specialization, and extinction on coral reefs

Coral reefs worldwide are being degraded because of global warming (coral bleaching) and coastal development (sedimentation and eutrophication). Predicting the risk of species extinctions from this type of habitat degradation is one of the most challenging and urgent tasks facing ecologists. Habitat specialists are thought to be more prone to extinction than generalists; however, specialists may be more susceptible to extinction because (1) they are specialists per se, (2) they are less abundant than generalists, or (3) both. Here, I show that declines in coral abundance lead to corresponding declines in the abundance of coral‐dwelling fishes, but with proportionally greater losses to specialists than generalists. In addition, specialists have smaller initial population sizes than generalists. Consequently, specialists face a dual risk of extinction because their already small populations decline more rapidly than those of generalists. Corresponding with this increased extinction risk, I describe the local extinction of one specialist species and the near‐global extinction of another species. I conclude that habitat specialists will be the first species lost from coral reefs because their small populations suffer the most from human‐induced disturbances.     

Climatic refugia and reduced extinction correlate with underdispersion in mammals and birds in Africa

Macroevolutionary patterns, often inferred from metrics of community relatedness, are often used to ascertain major evolutionary processes shaping communities. These patterns have been shown to be informative of biogeographic barriers, of habitat suitability and invasibility (especially with regard to environmental filtering), and of regions that function as evolutionary cradles (i.e., sources of diversification) or museums (i.e., regions of reduced extinction). Here, we analyzed continental datasets of mammal and bird distributions to identify primary drivers of community evolution on the African continent for mostly endothermic vertebrates. We find that underdispersion (i.e., relatively low phylogenetic diversity compared to species richness) closely correlates with specific ecoregions that have been identified as climatic refugia in the literature, regardless of whether these specific regions have been touted as cradles or museums. Using theoretical models of identical communities that differ only with respect to extinction rates, we find that even small suppressions of extinction rates can result in underdispersed communities, supporting the hypothesis that climatic stability can lead to underdispersion. We posit that large‐scale patterns of under‐ and overdispersion between regions of similar species richness are more reflective of a particular region’s extinction potential, and that the very nature of refugia can lead to underdispersion via the steady accumulation of species richness through diversification within the same ecoregion during climatic cycles. Thus, patterns of environmental filtering can be obfuscated by environments that coincide with biogeographic refugia, and considerations of regional biogeographic history are paramount for inferring macroevolutionary processes.     

Effects of local negative feedbacks on the evolution of species within metacommunities

Local negative feedbacks occur when the occupation of a site by a species decreases the subsequent fitness of related individuals compared to potential competitors. Such negative feedbacks can enhance diversity by changing the spatial structure of the environment. The conditions, however, involve dispersive, environmental and evolutionary processes in complex interactive ways. We introduce a model that accounts for four mechanisms: colonisation‐competition‐extinction ecological dynamics, evolutionary dynamics, local negative feedbacks and environmental averaging. Three qualitatively distinct dynamics are possible, one dominated by specialists, another dominated by generalists and an intermediate situation exhibiting taxon cycles. We discuss how metacommunity diversity, macro‐ecological patterns and environmental patterning are linked to the three qualitative dynamics. The model provides classical shapes for morph‐abundance distributions, or diversity‐area relationships. Diversity can be high when specialists dominate or when taxon cycles happen. Finally, local negative feedbacks often yield fine‐grain environments for taxon cycle dynamics and coarse‐grain environments when generalists dominate.     

Extinctions,traits and phylogenetic community structure: insights from primate assemblages in Madagascar

Understanding the origin and maintenance of community composition through ecological and evolutionary time has been a central challenge in ecology. However little is known about how extinction may alter patterns of phylogenetic and phenotypic structure within communities. To address this, we used past and present primate communities in Madagascar as our model system to explore how a large extinction event within a taxon may alter evolutionary relationships and phenotypic distributions within communities. We also explored the influence of environment on the structure of present‐day lemur communities. We found a phylogenetic pattern of overdispersion in both past and present‐day communities. However, trait structures, including relative dispersion of body masses and trophic niches were altered following extinction. We posit that the overdispersed phylogenetic patterns have resulted from the unique ecological and evolutionary history of Madagascar's primates including a rapid adaptive radiation in the presence of a broad niche‐space available during colonization. Differences in trait structures between present and past primate communities may be reflective of the selective extinction process that eliminated the largest primates from the island. Habitat also appeared to influence the structure of present‐day lemur communities. Lower divergence in patterns of phylogeny, body mass and activity rhythms were found in dry relative to wet habitats. This may be due to potential advantages of being small and nocturnal in environments with low productivity and hot dry climates. We suggest current studies exploring community processes should consider potential effects of past extinction events. Such work is important for understanding community assembly, coexistence, and mechanisms driving extinctions, particularly given the current extinction crisis facing ecosystems globally.     

Survival patterns of macrobenthic marine assemblages during the end-Permian mass extinction in the western Tethys (Dolomites, Italy)

The ecological competition between brachiopods and bivalves is analysed by means of a quantitative palaeoecologic method applied on four assemblages located within a short stratigraphic interval, approximately 2 m thick, in the lower Tesero Member of the Werfen Formation (in the Southern Alps). The assemblages originate from the Tesero, Bulla and Sass de Putia sections. The analysed stratigraphic interval, uppermost Changhsingian in age, is located between the early and heaviest phase of the end-Permian mass extinction, which occurred across the Bellerophon/Werfen formational boundary (Event Boundary), and the Permian/Triassic boundary (Chronological Boundary), when nearly all the Permian stenotopic holdovers disappeared.These assemblages are characterised by small sized skeletons (“Lilliput effect”), which represent an adaptive survival strategy in stressed and harsh habitats resulting from the climatic and palaeoceanographic changes connected with the mass extinction. The Tesero assemblages are dominated by rhynchonelliform brachiopod Orbicoelia (bed CNT10) or Streptorhynchus (bed CNT11A), which were mostly attached at the top of shallow microbialitic mounds. These assemblages are again dominated by Permian stenotopic taxa and show a Palaeozoic structure. The Tesero habitat, which again permitted the survival of brachiopods, represented one of the last refuges in the western Tethys. On the contrary, the Bulla (BU9-10) and Sass de Putia (wPK13A) assemblages are bivalve-dominated, and thus show an ecologic structure typical of Early Triassic post-extinction marine benthic communities or Palaeozoic stressed marine communities. The bivalve-dominated assemblages proliferated in prevailing muddy siliciclastic substrates, with brief episodes of microbial algal growth. The most important environmental limiting factors and leading causes of end-Permian mass extinction are discussed in terms of palaeoautecologic and palaeosynecologic analysis.The different taxonomic composition and ecologic structure of the assemblages is related to palaeogeography, including water depth and connections with the open sea. The brachiopod-dominated assemblage, exclusive of the Tesero section, proliferated in microbial carbonate habitats in near-shore environments. The bivalve-dominated assemblages, which were more widespread than the brachiopod assemblages in the Dolomites and also occurred in other western Tethys localities, occur in more open and deeper marine environments. In the western Tethys margins, the local distribution of mixed faunas suggests that the extinction of Permian stenotopic taxa was caused by the onset of poisonous water on the shelves originating from deep marine environments.This extinction pattern appears to be a regional phenomenon and does not seem be applicable on a global scale. The extinction events were controlled by a complex network of interactive factors and the survival of faunal elements was probably stochastic.     

Defining climate's role in ecosystem evolution: Clues from late quaternary mammals

Mammalian communities alter their taxonomic composition through time as the species composing them change their biogeographic range, become extinct, or evolve into new species. When taxonomic compositions change through these processes, inevitably the links between taxa and communities change too, resulting in evolution from one ecosystem into the next. Late Quaternary examples suggest that on a timescale encompassing a few thousand to a few hundred thousand years (the “multi‐millennial timescale"), climatic change is perhaps the most important driver of ecosystem evolution because it periodically forces biogeographic changes and extinction. Climatic change over this timescale, which essentially slips between “geological time”; and “ecological time”;, is not very closely in phase with population‐level evolution of a species analyzed for this study, the meadow vole Microtus pennsylvanicus; therefore climatic oscillations on the multi‐millennial timescale may not stimulate speciation much. Instead, speciation may contribute to ecosystem evolution independent of climatic change and over a longer time scale.     

The Colonisation of Exotic Species Does Not Have to Trigger Faunal Homogenisation: Lessons from the Assembly Patterns of Arthropods on Oceanic Islands

Human-caused disturbances can lead to the extinction of indigenous (endemic and native) species, while facilitating and increasing the colonisation of exotic species; this increase can, in turn, promote the similarity of species compositions between sites if human-disturbed sites are consistently invaded by a regionally species-poor pool of exotic species. In this study, we analysed the extent to which epigean arthropod assemblages of four islands of the Azorean archipelago are characterised by nestedness according to a habitat-altered gradient. The degree of nestedness represents the extent to which less ubiquitous species occur in subsets of sites occupied by the more widespread species, resulting in an ordered loss/gain of species across environmental or ecological gradients. A predictable loss of species across communities while maintaining others may lead to more similar communities (i.e. lower beta-diversity). In contrast, anti-nestedness occurs when different species tend to occupy distinct sites, thus characterising a replacement of species across such gradients. Our results showed that an increase in exotic species does not promote assemblage homogenisation at the habitat level. On the contrary, exotic species were revealed as habitat specialists that constitute new and well-differentiated assemblages, even increasing the species compositional heterogeneity within human-altered landscapes. Therefore, contrary to expectations, our results show that both indigenous and exotic species established idiosyncratic assemblages within habitats and islands. We suggest that both the historical extinction of indigenous species in disturbed habitats and the habitat-specialised character of some exotic invasions have contributed to the construction of current assemblages.     

The Southeast Saline Everglades revisited: 50 years of coastal vegetation change

Abstract. We examined the vegetation of the Southeast Saline Everglades (SESE), where water management and sea level rise have been important ecological forces during the last 50 years. Marshes within the SESE were arranged in well‐defined compositional zones parallel to the coast, with mangrove‐dominated shrub communities near the coast giving way to graminoid‐mangrove mixtures, and then Cladium marsh. The compositional gradient was accompanied by an interiorward decrease in total aboveground biomass, and increases in leaf area index and periphyton biomass. Since the mid‐1940s, the boundary of the mixed graminoid‐mangrove and Cladium communities shifted inland by 3.3 km. The interior boundary of a low‐productivity zone appearing white on both black‐and‐white and CIR photos moved inland by 1.5 km on average. A smaller shift in this ‘white zone’ was observed in an area receiving fresh water overflow through gaps in one of the SESE canals, while greater change occurred in areas cut off from upstream water sources by roads or levees. These large‐scale vegetation dynamics are apparently the combined result of sea level rise ‐ ca. 10 cm since 1940 ‐ and water management practices in the SESE.     

Hybridization during altitudinal range shifts: nuclear introgression leads to extensive cyto‐nuclear discordance in the fire salamander

Ecological models predict that, in the face of climate change, taxa occupying steep altitudinal gradients will shift their distributions, leading to the contraction or extinction of the high‐elevation (cold‐adapted) taxa. However, hybridization between ecomorphologically divergent taxa commonly occurs in nature and may lead to alternative evolutionary outcomes, such as genetic merger or gene flow at specific genes. We evaluate this hypothesis by studying patterns of divergence and gene flow across three replicate contact zones between high‐ and low‐elevation ecomorphs of the fire salamander (Salamandra salamandra) that have experienced altitudinal range shifts over the current postglacial period. Strong population structure with high genetic divergence in mitochondrial DNA suggests that vicariant evolution has occurred over several glacial–interglacial cycles and that it has led to cryptic differentiation within ecomorphs. In current parapatric boundaries, we do not find evidence for local extinction and replacement upon postglacial expansion. Instead, parapatric taxa recurrently show discordance between mitochondrial and nuclear markers, suggesting nuclear‐mediated gene flow across contact zones. Isolation with migration models support this hypothesis by showing significant gene flow across all five parapatric boundaries. Together, our results suggest that, while some genomic regions, such as the mitochondria, may follow morphologic species traits and retreat to isolated mountain tops, other genomic regions, such as nuclear markers, may flow across parapatric boundaries, sometimes leading to a complete genetic merger. We show that despite high ecologic and morphologic divergence over prolonged periods of time, hybridization allows for evolutionary outcomes alternative to extinction and replacement of taxa in response to climate change.     

Biogeography of the yeasts of ephemeral flowers and their insects

We studied specific yeast communities vectored by beetles, drosophilids, and bees that visit ephemeral flowers, mostly in the genus Hibiscus and in the families Convolvulaceae and Cactaceae, in the Neotropical, Nearctic, and Australian biogeographic regions. The communities consist mostly of yeasts in four clades centered around the genera Metschnikowia, Kodamaea, Wickerhamiella, and Starmerella. The largest geographic discontinuity occurs as a function of the nitidulid beetle species that dominate the non-pollinator insect visitors of the flowers. This partitions the New World, where the dominant beetle is in the genus Conotelus, from the Australian biogeographic region, dominated by species of Aethina. Distinct but sympatric insects may also carry radically different yeast communities.     

Opposing mechanisms affect taxonomic convergence between tree assemblages during tropical forest succession

Whether successional forests converge towards an equilibrium in species composition remains an elusive question, hampered by high idiosyncrasy in successional dynamics. Based on long‐term tree monitoring in second‐growth (SG) and old‐growth (OG) forests in Costa Rica, we show that patterns of convergence between pairs of forest stands depend upon the relative abundance of species exhibiting distinct responses to the successional gradient. For instance, forest generalists contributed to convergence between SG and OG forests, whereas rare species and old‐growth specialists were a source of divergence. Overall, opposing trends in taxonomic similarity among different subsets of species nullified each other, producing a net outcome of stasis over time. Our results offer an explanation for the limited convergence observed between pairwise communities and suggest that rare species and old‐growth specialists may be prone to dispersal limitation, while the dynamics of generalists and second‐growth specialists are more predictable, enhancing resilience in tropical secondary forests.     

Winter is coming: Miocene and Quaternary climatic shifts shaped the diversification of Western‐Mediterranean Harpactocrates (Araneae,Dysderidae) spiders

Past climatic shifts have played a major role in generating and shaping biodiversity. Quaternary glacial cycles are the better known examples of dramatic climatic changes endured by ecosystems in temperate regions. Although still a matter of debate, some authors suggest that glaciations promoted speciation. Here we investigate the effect of past climatic changes on the diversification of the ground‐dwelling spider genus Harpactocrates, distributed across the major mountain ranges of the western Mediterranean. Concatenated and species‐tree analyses of multiple mitochondrial and nuclear loci, combined with the use of fossil and biogeographic calibration points, reveal a Miocene origin of most nominal species, but also unravel several cryptic lineages tracing back to the Pleistocene. We hypothesize that the Miocene Climatic Transition triggered major extinction events in the genus but also promoted its subsequent diversification. Under this scenario, the Iberian mountains acted as an island‐like system, providing shelter to Harpactocrates lineages during the climate shifts and favouring isolation between mountain ranges. Quaternary glacial cycles contributed further to the diversification of the group by isolating lineages in peripheral refugia within mountain ranges. In addition, we recovered some unique biogeographic patterns, such as the colonization of the Alps and the Apennines from the Iberian Peninsula.     

The community structure of sessile heterotrophic bacteria stressed by acid mine drainage

Microbial communities that developed on glass slides suspended in acid-polluted (pH=2.9) and nonpolluted (pH=6.5) but otherwise similar waters showed evidence of stress when suspended at the opposite station. Glucose incorporation was inhibited in both translocated communities, but the inhibition was not as severe and recovery of activity was faster for the acid-developed community as compared to the circumneutral community. The communities contained a substantially different set of members with little overlap. The range of pH values at which the members of the acid-developed community could function suggested that the members of that community were generalists, as opposed to narrowly constrained members of the community from the circumneutral station. Based on the proportion of test characters that received positive responses, the organisms from the acidic site were more general in their abilities (47.6% positive) as compared with the neutral counterparts (18.7% positive). The results support the concept that communities developed in extreme environments tend to be generalists, whereas those from mesic environments, due to the higher levels of competition present, tend to be specialists. Furthermore, the study of microbial communities in dynamic systems such as streams and reservoir inflows is facilitated by the use of solid surfaces which allow an assemblage of nontransient microbes to develop.     

Elements of metacommunity structure in Amazonian Zygoptera among streams under different spatial scales and environmental conditions

An important aspect of conservation is to understand the founding elements and characteristics of metacommunities in natural environments, and the consequences of anthropogenic disturbance on these patterns. In natural Amazonian environments, the interfluves of the major rivers play an important role in the formation of areas of endemism through the historical isolation of species and the speciation process. We evaluated elements of metacommunity structure for Zygoptera (Insecta: Odonata) sampled in 93 Amazonian streams distributed in two distinct biogeographic regions (areas of endemism). Of sampled streams, 43 were considered to have experienced negligible anthropogenic impacts, and 50 were considered impacted by anthropogenic activities. Our hypothesis was that preserved (“negligible impact”) streams would present a Clementsian pattern, forming clusters of distinct species, reflecting the biogeographic pattern of the two regions, and that anthropogenic streams would present random patterns of metacommunity, due to the loss of more sensitive species and dominance of more tolerant species, which have higher dispersal ability and environmental tolerance. In negligible impact streams, the Clementsian pattern reflected a strong biogeographic pattern, which we discuss considering the areas of endemism of Amazonian rivers. As for communities in human‐impacted streams, a biotic homogenization was evident, in which rare species were suppressed and the most common species had become hyper‐dominant. Understanding the mechanisms that trigger changes in metacommunities is an important issue for conservation, because they can help create mitigation measures for the impacts of anthropogenic activities on biological communities, and so should be expanded to studies using other taxonomic groups in both tropical and temperate systems, and, wherever possible, at multiple spatial scales.     

Experimental demonstration of accelerated extinction in source‐sink metapopulations

Population extinction is a fundamental ecological process which may be aggravated by the exchange of organisms between productive (source) and unproductive (sink) habitat patches. The extent to which such source‐sink exchange affects extinction rates is unknown. We conducted an experiment in which metapopulation effects could be distinguished from source‐sink effects in laboratory populations of Daphnia magna. Time‐to‐extinction in this experiment was maximized at intermediate levels of habitat fragmentation, which is consistent with a minority of theoretical models. These results provided a baseline for comparison with experimental treatments designed to detect effects of concentrating resources in source patches. These treatments showed that source‐sink configurations increased population variability (the coefficient of variation in abundance) and extinction hazard compared with homogeneous environments. These results suggest that where environments are spatially heterogeneous, accurate assessments of extinction risk will require understanding the exchange of organisms among population sources and sinks. Such heterogeneity may be the norm rather than the exception because of both the intrinsic heterogeneity naturally exhibited by ecosystems and increasing habitat fragmentation by human activity.     

Local endemism and within‐island diversification of shrews illustrate the importance of speciation in building Sundaland mammal diversity

Island systems are important models for evolutionary biology because they provide convenient, discrete biogeographic units of study. Continental islands with a history of intermittent dry land connections confound the discrete definitions of islands and have led zoologists to predict (i) little differentiation of terrestrial organisms among continental shelf islands and (ii) extinction, rather than speciation, to be the main cause of differences in community composition among islands. However, few continental island systems have been subjected to well‐sampled phylogeographic studies, leaving these biogeographic assumptions of connectivity largely untested. We analysed nine unlinked loci from shrews of the genus Crocidura from seven mountains and two lowland localities on the Sundaic continental shelf islands of Sumatra and Java. Coalescent species delimitation strongly supported all currently recognized Crocidura species from Sumatra (six species) and Java (five species), as well as one undescribed species endemic to each island. We find that nearly all species of Crocidura in the region are endemic to a single island and several of these have their closest relative(s) on the same island. Intra‐island genetic divergence among allopatric, conspecific populations is often substantial, perhaps indicating species‐level diversity remains underestimated. One recent (Pleistocene) speciation event generated two morphologically distinct, syntopic species on Java, further highlighting the prevalence of within‐island diversification. Our results suggest that both between‐ and within‐island speciation processes generated local endemism in Sundaland, supplementing the traditional view that the region's fauna is relictual and primarily governed by extinction.     

Predictors of light-limited growth and competition of phytoplankton in a well-mixed water column

Based on a model of light limited growth, Huisman and Weissing found that in a well mixed water column with constant light supply (energy reaching the water surface), equilibrium growth and competition of phytoplankton for light can be characterised by a critical light intensity at the base of the column (I*out). The present study attempts to give a further insight into this model. We first analyse the dependence of the critical light intensity on four parameters: initial slope of the photosynthesis-intensity (p-I) curve, maximal photosynthetic rate, the light-saturated parameter Ikand specific carbon loss rate. Increases in the first two parameters tend to reduce the critical light intensity and increases in the last two tend to increase the critical light intensity. Then we analyse the performance of a model under variable light supply with a time-scale of 1 day (24 hr). Within this time-scale, the critical light intensity changes with time. However, the equilibrium growth and the outcome of competition for light can be adequately characterised by critical light extinction defined as the upper limit of total light extinction due to both biomass and non-living matter in the water column. Under constant light supply, a critical light intensity uniquely corresponds to a critical light extinction. Therefore, critical light extinction can be utilised to predict the equilibrium growth and the outcome of competition under both constant and variable light supply. By changing the maximal light supply at noon, seasonal succession of species composition of communities is investigated. The possible effect of two typical photoresponses, photoadaptation and photoinhibition, on growth and competiton are discussed. Copyright 1999 Academic Press.     

Patterns of species density and productivity at different spatial scales in herbaceous plant communities

A major challenge in evaluating patterns of species richness and productivity involves acquiring data to examine these relationships empirically across a range of ecologically significant spatial scales. In this paper, we use data from herb‐dominated plant communities at six Long‐Term Ecological Research (LTER) sites to examine how the relationship between plant species density and above‐ground net primary productivity (ANPP) differs when the spatial scale of analysis is changed. We quantified this relationship at different spatial scales in which we varied the focus and extent of analysis: (1) among fields within communities, (2) among fields within biomes or biogeographic regions, and (3) among communities within biomes or biogeographic regions. We used species density (D=number of species per m²) as our measure of diversity to have a comparable index across all sites and scales. Although we expected unimodal relationships at all spatial scales, we found that spatial scale influenced the form of the relationship. At the scale of fields within different grassland communities, we detected a significant relationship at only one site (Minnesota old‐fields), and it was negative linear. When we expanded the extent of analyses to biogeographic regions (grasslands or North America), we found significant unimodal relationships in both cases. However, when we combined data to examine patterns among community types within different biogeographic regions (grassland, alpine tundra, arctic tundra, or North America), we did not detect significant relationships between species density and ANPP for any region. The results of our analyses demonstrate that the spatial scale of analysis – how data are aggregated and patterns examined – can influence the form of the relationship between species density and productivity. It also demonstrates the need for data sets from a broad spectrum of sites sampled over a range of scales for examining challenging and controversial ecological hypotheses.     

AFLP analysis of genetic relationships in the genus Fosterella L.B. Smith (Pitcairnioideae, Bromeliaceae).

The neotropical genus Fosterella L.B. Smith (Pitcairnioideae, Bromeliaceae) comprises about 30 species, with a centre of diversity in semiarid to humid habitats of the Andean slopes and valleys of Bolivia. Morphologic differentiation of species is difficult because of a paucity of diagnostic characters, and little is known about the infrageneric phylogeny. Here, we present the results of an amplified fragment length polymorphism (AFLP) analysis of 77 Fosterella specimens, covering 18 recognized species and 9 as-yet undescribed morphospecies. Eight primer combinations produced 310 bands, which were scored as presence/absence characters. Neighbour-joining tree reconstruction revealed 12 clusters (A-L) with various levels of support. Well-supported species groups were also recovered by a principal coordinates analysis. With few exceptions, morphologically defined species boundaries were confirmed by the molecular data. Phylogenetic relationships between species groups remained ambiguous, however, because of short internal branch lengths. The AFLP data were complemented by a survey of the leaf anatomy of 19 Fosterella species. Species concepts and assemblages are discussed in the context of molecular, morphologic, anatomic, ecologic, and biogeographic data. The data suggest that accidental long-distance dispersal and founder events have been important for Fosterella speciation.