Energy and Biodiversity

"Latitudinal Gradients in Species Diversity": Reflections on Pianka's 1966 Article and a Look Forward.

The Central Yangtze ecoregion in China includes a number of lakes, but these have been greatly affected by human activities over the past several decades, resulting in severe loss of biodiversity. In this paper, we document the present distribution of the major lakes and the changes in size that have taken place over the past 50 years, using remote sensing data and historical observations of land cover in the region. We also provide an overview of the changes in species richness, community composition, population size and age structure, and individual body size of aquatic plants, fishes, and waterfowl in these lakes. The overall species richness of aquatic plants found in eight major lakes has decreased substantially during the study period. Community composition has also been greatly altered, as have population size and age and individual body size in some species. These changes are largely attributed to the integrated effects of lake degradation, the construction of large hydroelectric dams, the establishment of nature reserves, and lake restoration practices.

Planet Earth hosts an incredible biological diversity. Estimated numbers of species occurring on Earth range from 5 to 11 million eukaryotic species including 400,000-450,000 species of plants. Much of this biodiversity remains poorly known and many species have not yet been named or even been discovered. This is not surprising, as the majority of species is known to be rare and ecosystems are generally dominated by a limited number of common species.
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\nTropical rainforests are the most species-rich terrestrial ecosystems on Earth. The general higher level of species richness is often explained by higher levels of energy near the Equator (latitudinal diversity gradient). However, when comparing tropical rainforest biomes, African rainforests host fewer plant species than either South American or Asian ones. The Central African country of Gabon is situated in the Lower Guinean phytochorical region. It is largely covered by what is considered to be the most species-rich lowland rainforest in Africa while the government supports an active conservation program. As such, Gabon is a perfect study area to address that enigmatic question that has triggered many researchers before: “What determines botanical species richness?”.
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\nIn the past 2.5 million years, tropical rainforests have experienced 21 cycles of global glaciations. They responded to this by contracting during drier and cooler glacials into larger montane and smaller riverine forest refugia and expanding again during warmer and wetter interglacials. The current rapid global climate change coupled with change of land use poses new threats to the survival of many rainforest species. The limited availability of resources for conservation forces governments and NGOs to set priorities. Unfortunately, for many plant species, lack of data on their distribution hampers well-informed decision making in conservation.
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\nSpecies distribution models (SDMs) offer opportunities to bridge at least partly this knowledge gap. SDMs are correlative models that infer the spatial distribution of species using only a limited set of known species occurrence records coupled with high resolution environmental data. SDMs are widely applied to study the past, present and future distribution of species, assess the risk of invasive species, infer patterns of species richness and identify hotspots, as well as to assess the impact of climate change. The currently available methods form a pipeline, with which data are selected and cleaned, models selected, parameterized, evaluated and projected to other areas and climatic scenarios, and biodiversity patterns are computed from these SDMs. In this thesis, SDMs of all Gabonese plant species were generated and patterns of species richness and of weighted endemism were computed (chapter 4 & 5).
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\nAlthough this pipeline enables the rapid generation of SDMs and inferring of biodiversity patterns, its effective use is limited by several matters of which three are specifically addressed in this thesis. Not knowing the true distribution limits the opportunities to assess the accuracy of models and assess the impact of assumptions and limitations of SDMs. The use of simulated species has been advocated as a method to systematically assess the impact of specific matters of SDMs (virtual ecologist). Following this approach, in chapter 2, I present a novel method to simulate large numbers of species that each have their own unique niche.
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\nOne matter of SDMs that is usually ignored but has been shown to be of great impact on model accuracy is the number of species occurrence records used to train a model. In chapter 2, I quantify the effect of sample size on model accuracy for species of different range size classes. The results show that the minimum number of records required to generate accurate SDMs is not uniform for species of every range size class and that larger sample sizes are required for more widespread species. By applying a uniform minimum number of records, SDMs of narrow-ranged species are incorrectly rejected and SDMs of widespread species are incorrectly accepted. Instead, I recommend to identify and apply the unique minimum numbers of required records for each individual species. The method presented here to identify the minimum number of records for species of particular range size classes is applicable to any species group and study area.
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\nThe range size or prevalence is an important plant feature that is used in IUCN Red List classifications. It is commonly computed as the Extent Of Occurrence (EOO) and Area Of Occupancy (AOO). Currently, these metrics are computed using methods based on the spatial distribution of the known species occurrences. In chapter 3, using simulated species again, I show that methods based on the distribution of species occurrences in environmental parameter space clearly outperform those based on spatial data. In this chapter, I present a novel method that estimates the range size of a species as the fraction of raster cells within the minimum convex hull of the species occurrences, when all cells from the study area are plotted in environmental parameter space. This novel method outperforms all ten other assessed methods. Therefore, the current use of EOO and AOO based on spatial data alone for the purpose of IUCN Red List classification should be reconsidered. I recommend to use the novel method presented here to estimate the AOO and to estimate the EOO from the predicted distribution based on a thresholded SDM.
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\nIn chapter 4, I apply the currently best possible methods to generate accurate SDMs and estimate the range size of species to the large dataset of Gabonese plant species records. All significant SDMs are used here to assess the unique contribution of narrow-ranged, widespread, and randomly selected species to patterns of species richness and weighted endemism. When range sizes of species are defined based on their full range in tropical Africa, random subsets of species best represent the pattern of species richness, followed by narrow-ranged species. Narrow-ranged species best represent the weighted endemism pattern. Moreover, the results show that the applied criterion of widespread and narrow-ranged is crucial. Too often, range sizes of species are computed on their distribution within a study area defined by political borders. I recommend to use the full range size of species instead. Secondly, the use of widespread species, of which often more data are available, as an indicator of diversity patterns should be reconsidered.
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\nThe effect of global climate change on the distribution patterns of Gabonese plant species is assed in chapter 5 using SDMs projected to the year 2085 for two climate change scenarios assuming either full or no dispersal. In Gabon, predicted loss of plant species ranges from 5% assuming full dispersal to 10% assuming no dispersal. However, these numbers are likely to be substantially higher, as for many rare, narrow-ranged species no significant SDMs could be generated. Predicted species turnover is as high as 75% and species-rich areas are predicted to loose many species. The explanatory power of individual future climate anomalies to predicted future species richness patterns is quantified. Species loss is best explained by increased precipitation in the dry season. Species gain and species turnover are correlated with a shift from extreme to average values of annual temperature range.
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\nIn the final chapter, the results are placed in a wider scientific context. First, the results on the methodological aspects of SDMs and their implications of the SDM pipeline are discussed. The method presented in this thesis to simulate large numbers of species offers opportunities to systematically investigate other matters of the pipeline, some of which are discussed here. Secondly, the factors that shape the current and predicted future patterns of plant species richness in Gabon are discussed including the location of centres of species richness and of weighted endemism in relation to the hypothesized location of glacial forest refugia. Factors that may contribute to the lower species richness of African rainforests compared with South American and Asian forests are discussed. I conclude by reflecting on the conservation of the Gabonese rainforest and its plant species as well as on the opportunities SDMs offer for this in the wider socio-economic context of a changing world with growing demand for food and other ecosystem services.

Summary1. Although a latitudinal gradient in species diversity has been observed for various taxa, the factors generating the latitudinal gradient at broad spatial scales are difficult to identify because several candidate factors change simultaneously with latitude. We investigated latitudinal gradients in stream invertebrate assemblages in 30 headwater streams in Hokkaido Island, Japan, focusing on the regional scale to discount historical factors and to extract the effects of environmental factors on latitudinal gradients in diversity.2. Taxon diversity (Shannon index) and taxon richness (number of taxa per unit area) increased with latitude. Abundance showed a similar latitudinal gradient, whereas evenness (Δ1) did not. Hence, we conclude that the observed latitudinal gradient in taxon richness was generated by directional variation in abundance (passive accumulation), leading to that in taxon diversity.3. Precipitation, which is strongly related to flood disturbances, decreased with latitude and was an important factor explaining variation in taxon diversity, taxon richness and abundance. The probability of a taxon being present tended to increase from south to north, suggesting that the higher taxon richness observed in northern sites may be because of the presence of rare species. These findings indicate that flood disturbance varying with latitude may influence abundance and local extinction rates of rare species, consequently affecting taxon richness and taxon diversity.4. By detecting the effects of an environmental factor (precipitation) on the latitudinal gradients in taxon diversity and taxon richness without interference by historical factors, this study demonstrates processes that can produce latitudinal gradients in the diversity of stream invertebrate assemblages.

Biological diversity

Aim The aim of this study was to test a variant of the evolutionary time hypothesis for the bird latitudinal diversity gradient derived from the effects of niche conservatism in the face of global climate change over evolutionary time.Location The Western Hemisphere.Methods We used digitized range maps of breeding birds to estimate the species richness at two grain sizes, 756 and 12,100 km2. We then used molecular phylogenies resolved to family to quantify the root distance (RD) of each species as a measure of its level of evolutionary development. Birds were classified as ‘basal’ or ‘derived’ based on the RD of their family, and richness patterns were contrasted for the most basal and most derived 30% of species. We also generated temperature estimates for the Palaeogene across the Western Hemisphere to examine how spatial covariation between past and present climates might make it difficult to distinguish between ecological and evolutionary hypotheses for the current richness gradient.Results The warm, wet tropics support many species from basal bird clades, whereas the northern temperate zone and cool or dry tropics are dominated by species from more recent, evolutionarily derived clades. Furthermore, crucial to evaluating how niche conservatism among birds may drive the hemispherical richness gradient, the spatial structure of the richness gradient for basal groups is statistically indistinguishable from the overall gradient, whereas the richness gradient for derived groups is much shallower than the overall gradient. Finally, modern temperatures and the pattern of climate cooling since the Eocene are indistinguishable as predictors of bird species richness.Main conclusions Differences in the richness gradients of basal vs. derived clades suggest that the hemispherical gradient has been strongly influenced by the differential extirpation of species in older, warm‐adapted clades from parts of the world that have become cooler in the present. We propose that niche conservatism and global‐scale climate change over evolutionary time provide a parsimonious explanation for the contemporary bird latitudinal diversity gradient in the New World, although dispersal limitation of some highly derived clades probably plays a secondary role.

Determinants of orchid species diversity in world islands.

In the 1960s the new technique of gel electrophoresis revealed what was then considered to be an astonishing amount of molecular variation in natural populations, with about 30% of genetic loci being polymorphic. It was thought at the time that natural selection the dominant principle in evolutionary biology could not account for such high levels of variability the costs of selection would be too high. This prompted the proposal of the neutral theory of molecular evolution (Kimura 1968; King & Jukes 1969; Kimura 1983), which postulated that most molecular evolution did not involve natural selection at all: in this model, selectively neutral mutations arose and their frequencies simply fluctuated at random, as is inevitable in a finite population. Tropical forests pose a similar puzzle for ecologists. The enormous numbers of species seem to challenge our classical notions that coexistence requires that each species has its own unique niche: how can so many species construct unique niches from such a small number of requirements sun, water, a patch of ground? The same puzzle in a different context became known as the 'paradox of the plankton' (Hutchinson 1961). As in molecular evolution, so too in ecology a neutral theory has been proposed which may resolve our puzzle (Bell 2001; Hubbell 2001) and is attracting much attention. The theory's advocates have more in mind than tropical trees, but I will restrict myself to trees to make the discussion specific. This was the context in which the theory was first proposed (Hubbell 1979) and one of the main biological areas where we have a puzzle apparently requiring a radical solution. Hereafter I will refer to the neutral theory of biodiversity as NTB. The underlying stochastic theory is the same in the two areas, although it has been studied for much longer in population genetics, as neutral advocates point out (Hubbell 2001; Volkov et al. 2003). This means we can import many results from the population genetics literature, simply interpreting the biology in a different way. In this paper I will import an important result concerning the time-scale of the neutral process, which raises serious difficulties for the NTB as an explanation of tropical forest diversity. This difficulty has been noted before (Leigh 1999; Lande et al. 2003), but does not appear to be as widely known as it should. Nonetheless, as I will discuss, neutral theory can still provide useful null models for the interpretation of data. In the fir t section, I gather together some basic theoretical results that are common to both population genetics and NTB. This is for two reasons. First of all, it serves to emphasize that we really are talking about the same theory, giving us the confidence to bring into the body of NTB an important result from population genetics concerning the time-scale of the neutral process. This will be done in the third section. Secondly, people may find it useful to have these basic results gathered toget er in one place they are currently somewhat scattered about. Having emphasized the underlying identity of the theory, I then briefly explore the implications of the biological differences between the worlds of molecular evolution and biodiversity for the likely future development of the theory in the biodiversity context.

Migratory species use multiple habitats types and ecosystems to complete their life cycles, which exposes them to multiple human-caused stressors along their migratory routes. Overexploitation, habitat degradation, invasive species and connectivity loss have contributed to the decrease of migratory fishes globally in particular diadromous fishes that migrate between marine and freshwater systems. Therefore, understanding the joint impacts from anthropogenic disturbances and climate change on different habitats (e.g., both feeding and spawning grounds) and habitat connectivity (e.g., migration routes) is important for conserving migratory fish. Management will be most effective when management scales match ecological scales. This is particularly important for conserving migratory species, because of the requirement of multiple connected habitats that may cross local management boundaries. The main goals of this Ph.D. thesis are to quantify the impacts of multiple stressors on migratory fish species and prioritize management actions for conserving populations (chapters 2 & 3), species (chapter 4), and communities (chapter 5).A central challenge for managing diadromous fishes (species that migrate between freshwater and saltwater ecosystems) is to quantify increases in population persistence from actions that improve connectivity or reduce fishing mortality. In chapter 2, I used a population dynamic model and fish movement data to predict the interactive impacts of fishing pressure and connectivity loss by human modification of river flows on Australian bass Percalates novemaculeata. Then, in chapter 3, the monetary cost of management actions which included seasonal closures and restoring connectivity, were included in the model to find the most cost-effective way to conserve this fish population. The results reveal that the cost-effectiveness of management actions may vary with river flow and fishing pressure before implementing management actions, and implementation times. The spatiotemporal dynamics of how fish species and key resource users (i.e., anglers) respond to management actions can influence the effectiveness of management strategies. Flexible management plans and increased cooperation between water and fishery managers can be used to achieve the most effective balance between conserving migratory fish populations and minimising cost.Migratory species are particularly vulnerable to climate change as they occupy different ecosystems, as well as transitional habitat which are all impacted by climate change differently. Anthropogenic barriers can further reduce the ability of species to respond to a shifting climate. In chapter 4, I assessed the impact of climate change on the distribution of a migratory fish species, Australian grayling Prototroctes maraena, and how it affected priorities for restoring connectivity. I found climate change moves at different rates in marine and freshwater systems, decoupling the habitats used by grayling. In addition, the changing spatial distribution of suitable habitats in marine and freshwater systems altered the degree the species was exposed to other anthropogenic disturbances and changed the priorities for where to restore connectivity.In ecosystems that are vulnerable to human impacts, understanding how species assemblages respond to multiple disturbances is a key issue for conservation and environmental management. In chapter 5, I examined changes in fish community structure in Fiji, in response to deforestation, anthropogenic barriers and introduced species. My findings suggest that species traits can be used to predict species loss in modified environments, helps identify the impact of partially-confounded disturbances and may ultimately help tailor conservation actions for the most vulnerable species. This thesis disentangles the interacting impacts of multiple disturbances on migratory species. It outlines a quantitative approach to evaluate the cost-effectiveness of management actions, and the impacts of disturbances across different ecological and management scales. Simple but spatial explicit population model, habitat suitability model and trait-based surrogate were used to overcome the lack of adequate data for non-salmon diadromous species. In a broader sense, it demonstrates that by integrating stressors throughout a species’ life cycle can help to optimise conservation effort for migratory species.

The merits of neutral theory

Rising temperatures, changed precipitation patterns, and extreme weather are some of the ways that climate change is endangering biodiversity worldwide. This review looks at changes in species distribution, disturbances to ecosystem function, and methods to improve resilience in the face of these difficulties. This review evaluates how biodiversity and ecosystem resilience are pretentious by climate change, emphasising important pathways and pointing out knowledge gaps to direct future studies toward practical mitigation and adaptation measures. In addition to direct effects on species physiology, this review sought to identify specific ways that climate change factors, such as rising temperatures, altered precipitation patterns, and extreme weather events, are affecting biodiversity through indirect effects on species interactions and habitat availability. The implications of Climate Change (CC)on biodiversity are examined in this review, with a focus on how critical it is to comprehend and mitigate these effects. The review study explores the impacts of ocean acidification, habitat loss, rising temperatures, and shifts in species distribution and migration patterns. The need for resilient ecosystems through conservation techniques and sustainable practices to buffer negative consequences is increased by climate change, which has a large influence on global biodiversity by causing habitat loss, species migration, and ecosystem deterioration. Future scope entails carrying out long-term biodiversity monitoring in many habitats, which will yield important information on the long-term impacts of CC. This can contribute to recognising the most vulnerable species and ecosystems as well as trends and patterns in the dynamics of biodiversity.

William Solecki,1,a Cynthia Rosenzweig,2,a Reginald Blake,3,a Alex de Sherbinin,4 Tom Matte,5 Fred Moshary,6 Bernice Rosenzweig,7 Mark Arend,6 Stuart Gaffin,8 Elie Bou-Zeid,9 Keith Rule,10 Geraldine Sweeny,11 and Wendy Dessy11 1City University of New York, CUNY Institute for Sustainable Cities, New York, NY. 2Climate Impacts Group, NASA Goddard Institute for Space Studies, Center for Climate Systems Research, Columbia University Earth Institute, New York, NY. 3Physics Department, New York City College of Technology, CUNY, Brooklyn, NY; Climate Impacts Group, NASA Goddard Institute for Space Studies. 4 Center for International Earth Science Information Network (CIESIN), Columbia University, Palisades, NY. 5New York City Department of Health and Mental Hygiene, New York, NY. 6NOAA CREST, City College of New York, CUNY, New York, NY. 7CUNY Environmental Crossroads, City College of New York, CUNY, New York, NY. 8Center for Climate Systems Research, Columbia University Earth Institute, New York, NY. 9Department of Civil & Environmental Engineering, Princeton University, Princeton, NJ. 10Princeton Plasma Physics Laboratory, Princeton, NJ. 11New York City Mayor’s Office of Operation, New York, NY

The latitudinal diversity gradient (LDG) is one of the most extensive and important biodiversity patterns on the Earth. Various studies have established that species diversity increases with higher taxa numbers from the polar to the tropics. Studies of multicellular biotas have supported the LDG patterns from land (e.g., plants, animals, forests, wetlands, grasslands, fungi, and so forth) to oceans (e.g., marine organisms from freshwater invertebrates, continental shelve, open ocean, even to the deep sea invertebrates). So far, there are several hypotheses proposed to explore the diversity patterns and mechanisms of LDG, however, there has been no consensus on the underlying causes of LDG over the past few decades. Thus, we reviewed the progress of LDG studies in recent years. Although several explanations for the LDG have been proposed, these hypotheses are only based on species richness, evolution and the ecosystems. In this review, we summarize the effects of evolution and ecology on the LDG patterns to synthesize the formation mechanisms of the general biodiversity distribution patterns. These intertwined factors from ecology and evolution in the LDG are generally due to the wider distribution of tropical areas, which hinders efforts to distinguish their relative contributions. However, the mechanisms of LDG always engaged controversies, especially in such a context that the human activity and climate change has affected the biodiversity. With the development of molecular biology, more genetic/genomic data are available to facilitate the estimation of global biodiversity patterns with regard to climate, latitude, and other factors. Given that human activity and climate change have inevitably impacted on biodiversity loss, biodiversity conservation should focus on the change in LDG pattern. Using large-scale genetic/genomic data to disentangle the diversity mechanisms and patterns of LDG, will provide insights into biodiversity conservation and management measures. Future perspectives of LDG with integrative genetic/genomic, species, evolution, and ecosystem diversity patterns, as well as the mechanisms that apply to biodiversity conservation, are discussed. It is imperative to explore integrated approaches for recognizing the causes of LDG in the context of rapid loss of diversity in a changing world.

AimThe latitudinal diversity gradient (LDG) is a consequence of evolutionary and ecological mechanisms acting over long history, and thus is best investigated with organisms that have rich fossil records. However, combined neontological‐palaeontological investigations are mostly limited to large, shelled invertebrates, which keeps our mechanistic understanding of LDGs in its infancy. This paper aims to describe the modern meiobenthic ostracod LDG and to explore the possible controlling factors and the evolutionary mechanisms of this large‐scale biodiversity pattern.LocationPresent‐day Western North Atlantic.TaxonOstracoda.MethodsWe compiled ostracod census data from shallow‐marine environments of the western North Atlantic Ocean. Using these data, we documented the marine LDG with multiple metrics of alpha, beta (nestedness and turnover) and gamma diversity, and we tested whether macroecological patterns could be governed by different environmental factors, including temperature, salinity, dissolved oxygen, pH and primary productivity. We also explored the geologic age distribution of ostracod genera to investigate the evolutionary mechanisms underpinning the LDG.ResultsOur results show that temperature and climatic niche conservatism are important in setting LDGs of these small, poorly dispersing organisms. We also found evidence for some dispersal‐driven spatial dynamics in the ostracod LDG. Compared to patterns observed in marine bivalves, however, dispersal dynamics were weaker and they were bi‐directional, rather than following the ‘out‐of‐the‐tropics’ model.Main conclusionsOur detailed analyses revealed that meiobenthic organisms, which comprise two‐thirds of marine diversity, do not always follow the same rules as larger, better‐studied organisms. Our findings suggest that the understudied majority of biodiversity may be more sensitive to climate than well‐studied, large organisms. This implies that the impacts of ongoing Anthropocene climatic change on marine ecosystems may be much more serious than presently thought.

A decline in species richness moving from equatorial regions to polar regions is a common, but not universal, macroecological pattern. Many studies have focused on this pattern, but few have focused on how the vital rates responsible for species richness patterns, local rates of species extinction and turnover, vary with latitude. We examine patterns of richness, turnover and extinction in North American avian communities inhabiting three ecoregions, using methods that account for failure to detect all species present. We use breeding bird point count data from > 1000 routes in the Breeding Bird Survey collected from 1982 to 2001 to estimate richness, extinction probability and turnover rates. Our analyses differ from others in 1) the use of annual estimates derived at specific locations rather than index data accumulated over numbers of years, 2) the use of estimators that incorporated detection probabilities and 3) a focus on dynamical processes (colonization, extinction) in addition to static patterns (species richness). We find average species richness estimates (48 to 135 species) increasing with latitude for all three regions, contradicting predictions based on the latitudinal diversity gradient. The estimated rates of extinction and turnover declined with latitude across the three ecoregions. We speculate that higher richness might be linked to periods of superabundant food supply in northern areas that support greater numbers of resident and migrant species. Our primary ecological conclusions are that the latitudinal gradient in species richness is reversed for North American birds in the studied ecoregions, and that both local extinction and turnover decrease from southern to northern latitudes. Thus, the vital rates that determine richness show evidence of greater stability and reduced dynamics in northern areas of higher richness. We recommend additional studies examining patterns of colonization, extinction and turnover in communities, that use clearly defined estimators that deal with detection probability.