Landscape dynamics are widely thought to govern the tempo and mode of continental radiations, yet the effects of river network rearrangements on dispersal and lineage diversification remain poorly ...understood. We integrated an unprecedented occurrence dataset of 4,967 species with a newly compiled, time-calibrated phylogeny of South American freshwater fishes-the most species-rich continental vertebrate fauna on Earth-to track the evolutionary processes associated with hydrogeographic events over 100 Ma. Net lineage diversification was heterogeneous through time, across space, and among clades. Five abrupt shifts in net diversification rates occurred during the Paleogene and Miocene (between 30 and 7 Ma) in association with major landscape evolution events. Net diversification accelerated from the Miocene to the Recent (c. 20 to 0 Ma), with Western Amazonia having the highest rates of in situ diversification, which led to it being an important source of species dispersing to other regions. All regional biotic interchanges were associated with documented hydrogeographic events and the formation of biogeographic corridors, including the Early Miocene (c. 23 to 16 Ma) uplift of the Serra do Mar and Serra da Mantiqueira and the Late Miocene (c. 10 Ma) uplift of the Northern Andes and associated formation of the modern transcontinental Amazon River. The combination of high diversification rates and extensive biotic interchange associated with Western Amazonia yielded its extraordinary contemporary richness and phylogenetic endemism. Our results support the hypothesis that landscape dynamics, which shaped the history of drainage basin connections, strongly affected the assembly and diversification of basin-wide fish faunas.
The climatic variability hypothesis posits that the magnitude of climatic variability increases with latitude, elevation, or both, and that greater variability selects for organisms with broader ...temperature tolerances, enabling them to be geographically widespread. We tested this classical hypothesis for the elevational range sizes of more than 16,500 terrestrial vertebrates on 180 montane gradients. In support of the hypothesis, mean elevational range size was positively correlated with the scope of seasonal temperature variation, whereas elevational range size was negatively correlated with daily temperature variation among gradients. In accordance with a previous life history model and our extended versions of it, our findings indicate that physiological specialization may be favored under shorter-term climatic variability.
•Range shifts are increasingly influencing marine biodiversity and resources.•Here we define range extensions and contractions as stages.•Range shifts can be staged with multiple evidence types and ...applied to diverse species.•Relative range extension and contraction rates should be calculated for equivalent stages.•Assigning confidence to shifts with a stage-based framework may underpin ecological insights.
Climate change is transforming the structure of biological communities through the geographic extension and contraction of species’ ranges. Range edges are naturally dynamic, and shifts in the location of range edges occur at different rates and are driven by different mechanisms. This leads to challenges when seeking to generalize responses among taxa and across systems. We focus on warming-related range shifts in marine systems to describe extensions and contractions as stages. Range extensions occur as a sequence of (1) arrival, (2) population increase, and (3) persistence. By contrast, range contractions occur progressively as (1) performance decline, (2) population decrease and (3) local extinction. This stage-based framework can be broadly applied to geographic shifts in any species, life-history stage, or population subset. Ideally the probability of transitioning through progressive range shift stages could be estimated from empirical understanding of the various factors influencing range shift rates. Nevertheless, abundance and occupancy data at the spatial resolution required to quantify range shifts are often unavailable and we suggest the pragmatic solution of considering observations of range shifts within a confidence framework incorporating the type, amount and quality of data. We use case studies to illustrate how diverse evidence sources can be used to stage range extensions and contractions and assign confidence that an observed range shift stage has been reached. We then evaluate the utility of trait-based risk (invasion) and vulnerability (extinction) frameworks for application in a range shift context and find inadequacies, indicating an important area for development. We further consider factors that influence rates of extension and contraction of range edges in marine habitats. Finally, we suggest approaches required to increase our capacity to observe and predict geographic range shifts under climate change.
1. We examined in situ diversity and distribution of vascular epiphytes, as well as site environmental variables at six sites along a continuous elevational gradient (30-2600 m a.s.l.) of old-growth ...forest in Costa Rica. 2. A total of 555 species of vascular epiphytes from 130 genera of 53 families were identified to species or morphospecies. The ferns were the most diverse group, with 138 species, followed by orchids (112 species). Cloud forest at 1000 m was the richest site, representing the maximum of a pronounced mid-elevation peak in epiphyte species richness. 3. Spatial randomizations of recorded elevational ranges suggest that the overall elevational richness pattern of most epiphyte groups on this transect is substantially influenced by the mid-domain effect (MDE, the mid-elevation overlap of large-ranged species). Among the environmental factors considered (rainfall, temperature and canopy light environment), only rainfall was significantly correlated with richness. 4. Different patterns of richness for vascular epiphytes and for trees indicate that mechanisms differ between life forms. 5. We collected 26% of the estimated epiphyte species of Costa Rica along a single mountain transect. This, together with the finding that different groups and life forms varied in the elevation at which species richness peaked, highlights the need to conserve the few remaining intact elevational gradients in Latin America.
A wide variety of similarity indices for comparing two assemblages based on species incidence (i.e., presence/absence) data have been proposed in the literature. These indices are generally based on ...three simple incidence counts: the number of species shared by two assemblages and the number of species unique to each of them. We provide a new probabilistic derivation for any incidence‐based index that is symmetric (i.e., the index is not affected by the identity ordering of the two assemblages) and homogeneous (i.e., the index is unchanged if all counts are multiplied by a constant). The probabilistic approach is further extended to formulate abundance‐based indices. Thus any symmetric and homogeneous incidence index can be easily modified to an abundance‐type version. Applying the Laplace approximation formulas, we propose estimators that adjust for the effect of unseen shared species on our abundance‐based indices. Simulation results show that the adjusted estimators significantly reduce the biases of the corresponding unadjusted ones when a substantial fraction of species is missing from samples. Data on successional vegetation in six tropical forests are used for illustration. Advantages and disadvantages of some commonly applied indices are briefly discussed.
The causes of global variation in species richness have been debated for nearly two centuries with no clear resolution in
sight. Competing hypotheses have typically been evaluated with correlative ...models that do not explicitly incorporate the mechanisms
responsible for biotic diversity gradients. Here, we employ a fundamentally different approach that uses spatially explicit
Monte Carlo models of the placement of cohesive geographical ranges in an environmentally heterogeneous landscape. These models
predict species richness of endemic South American birds (2248 species) measured at a continental scale. We demonstrate that
the principal single-factor and composite (species-energy, water-energy and temperature-kinetics) models proposed thus far
fail to predict (, ⩽0.05) the richness of species with small to moderately large geographical ranges (first three range-size quartiles). These
species constitute the bulk of the avifauna and are primary targets for conservation. Climate-driven models performed reasonably
well only for species with the largest geographical ranges (fourth quartile) when range cohesion was enforced. Our analyses
suggest that present models inadequately explain the extraordinary diversity of avian species in the montane tropics, the
most species-rich region on Earth. Our findings imply that correlative climatic models substantially underestimate the importance
of historical factors and small-scale niche-driven assembly processes in shaping contemporary species-richness patterns.
Quaternary glacial–interglacial cycles repeatedly forced thermal zones up and down the slopes of mountains, at all latitudes. Although no one doubts that these temperature cycles have left their ...signature on contemporary patterns of geography and phylogeny, the relative roles of ecology and evolution are not well understood, especially for the tropics. To explore key mechanisms and their interactions in the context of chance events, we constructed a geographical range-based, stochastic simulation model that incorporates speciation, anagenetic evolution, niche conservatism, range shifts and extinctions under late Quaternary temperature cycles along tropical elevational gradients. In the model, elevational patterns of species richness arise from the differential survival of founder lineages, consolidated by speciation and the inheritance of thermal niche characteristics. The model yields a surprisingly rich variety of realistic patterns of phylogeny and biogeography, including close matches to a variety of contemporary elevational richness profiles from an elevational transect in Costa Rica. Mountaintop extinctions during interglacials and lowland extinctions at glacial maxima favour mid-elevation lineages, especially under the constraints of niche conservatism. Asymmetry in temperature (greater duration of glacial than of interglacial episodes) and in lateral area (greater land area at low than at high elevations) have opposing effects on lowland extinctions and the elevational pattern of species richness in the model—and perhaps in nature, as well.
Estimating the species, phylogenetic, and functional diversity of a community is challenging because rare species are often undetected, even with intensive sampling. The Good-Turing frequency ...formula, originally developed for cryptography, estimates in an ecological context the true frequencies of rare species in a single assemblage based on an incomplete sample of individuals. Until now, this formula has never been used to estimate undetected species, phylogenetic, and functional diversity. Here, we first generalize the Good-Turing formula to incomplete sampling of two assemblages. The original formula and its two-assemblage generalization provide a novel and unified approach to notation, terminology, and estimation of undetected biological diversity. For species richness, the Good-Turing framework offers an intuitive way to derive the non-parametric estimators of the undetected species richness in a single assemblage, and of the undetected species shared between two assemblages. For phylogenetic diversity, the unified approach leads to an estimator of the undetected Faith's phylogenetic diversity (PD, the total length of undetected branches of a phylogenetic tree connecting all species), as well as a new estimator of undetected PD shared between two phylogenetic trees. For functional diversity based on species traits, the unified approach yields a new estimator of undetected Walker et al.'s functional attribute diversity (FAD, the total species-pairwise functional distance) in a single assemblage, as well as a new estimator of undetected FAD shared between two assemblages. Although some of the resulting estimators have been previously published (but derived with traditional mathematical inequalities), all taxonomic, phylogenetic, and functional diversity estimators are now derived under the same framework. All the derived estimators are theoretically lower bounds of the corresponding undetected diversities; our approach reveals the sufficient conditions under which the estimators are nearly unbiased, thus offering new insights. Simulation results are reported to numerically verify the performance of the derived estimators. We illustrate all estimators and assess their sampling uncertainty with an empirical dataset for Brazilian rain forest trees. These estimators should be widely applicable to many current problems in ecology, such as the effects of climate change on spatial and temporal beta diversity and the contribution of trait diversity to ecosystem multi-functionality.
Ecologists and biogeographers usually rely on a single phylogenetic tree to study evolutionary processes that affect macroecological patterns. This approach ignores the fact that each phylogenetic ...tree is a hypothesis about the evolutionary history of a clade, and cannot be directly observed in nature. Also, trees often leave out many extant species, or include missing species as polytomies because of a lack of information on the relationship among taxa. Still, researchers usually do not quantify the effects of phylogenetic uncertainty in ecological analyses. We propose here a novel analytical strategy to maximize the use of incomplete phylogenetic information, while simultaneously accounting for several sources of phylogenetic uncertainty that may distort statistical inferences about evolutionary processes. We illustrate the approach using a clade-wide analysis of the hummingbirds, evaluating how different sources of uncertainty affect several phylogenetic comparative analyses of trait evolution and biogeographic patterns. Although no statistical approximation can fully substitute for a complete and robust phylogeny, the method we describe and illustrate enables researchers to broaden the number of clades for which studies informed by evolutionary relationships are possible, while allowing the estimation and control of statistical error that arises from phylogenetic uncertainty. Software tools to carry out the necessary computations are offered.
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