Introductory Chapter: Factors That Affect Biodiversity and Species Richness of Ecosystems - A Review

1. Introduction

The general latitudinal trend is that species diversity declines as latitude increases [1]. This appears to be the case for almost all terrestrial plants and animals [2, 3]. It is also usually used for the distribution of marine species [4, 5]. This latitudinal pattern in species richness is detectable in different spatial scales, habitats, and taxonomic groups [6]. However, because of the lack of agreement on the dynamics of site-to-site heterogeneity in species composition (b-diversity) through latitudinal gradients, latitudinal variations in species co-occurrence remain a central issue in ecology [7, 8]. Living species colonized and changed nearly all aquatic and terrestrial ecosystems on Earth, and thereby developed in their many shapes, physiology, and life history from origins more than three billion years ago. Ecosystems are not uniformly rich in species but this richness shows pattern across the world, and observers have long been puzzled about the origins of striking diversity trends such as the latitudinal diversity gradient, elevational gradients in terrestrial ecosystems, and bathymetric gradients in the sea. Since Darwin and Wallace, biologists have been focused on elucidating the mechanisms that lead to diversity. To explain why some regions of the world host greater numbers of taxa than other areas, studies on lineage differentiation and longevity (evolutionary biology) and organismal survivorship and coexistence (ecology, etc.) must be combined. In the last decade or so, new data on the pattern of biodiversity, fine-scale maps of climate and environmental factors, and huge developments in the reconstruction of the tree of life have been ongoing. Biogeographical and phylogenetic data integrations also restructured the patterns of the global distribution of species diversity as well as phylogenetic connections of organisms on various taxonomic scales. The processes that underlie species diversity trends are crucial to study, particularly when people influence important environmental changes [9]. Humans are diminishing habitat space for the majority of the world’s organisms, while global temperature and precipitation regimes are shifting, and these factors are in the focus of many hypotheses describing the nature and maintenance of species diversity. To complicate things, some of these assumptions involve the same factors, namely geographic area, energy climate stability, and biotic interactions, and generate similar predictions about diversity and the rate of speciation because most of the hypothetical factors coincide with the latitude. However, the intense theoretical and methodological attention focused on species richness gradients has not been applied to consider the broadscale distribution of other essential components of biodiversity, such as intraspecific diversity. Intraspecific diversity—whether defined as functional diversity, phylogenetic diversity, population richness, or genetic diversity within and among populations—can influence species’ geographic distributions and responses to environmental change [10, 11, 12, 13], community structure, and ecosystem functioning [14, 15]. Given the alarming pace of species loss and human modification of natural ecosystems, the importance to quantify biodiversity is crucial (e.g., [16, 17, 18, 19, 20]). Species richness, namely the number of species per unit area, is perhaps the simplest and most often used indicator of biological diversity. A substantial amount of biological research has been done using species richness as a metric to explain what causes, and is caused by, biodiversity. Species richness is often used as a measure of diversity within a single biological community, ecosystem, or habitat (e.g., [21]). Pianka [22] wrote the first review paper on large-scale diversity gradients and reviewed major hypotheses to explain the latitudinal diversity gradient. Latitudinal gradients have been known for almost a century in species diversity, and nowadays, some of these polar-equatorial patterns have been explored in depth and several authors added new hypotheses to explain latitudinal gradients [8, 23, 24]. The gradient-forming drivers are differentiated on the basis of significance to different stages of lineage divarication, survival, and allopatric; parapatric and sympatric speciation can be integrated into this framework [25].

2. Abiotic factors

When a population of a certain taxon extends, its range to an extra-tropical area has to face evolutionary trade-offs that influence speciation. Cold tolerance is the most important trait to avoid frost damage poleward from frost line, in the cold season species without frost tolerance can be easily eliminated, even if freezing does not occur every year. Significant energy must be invested in frost resistance at the expanse of growth and reproduction [26]. Thus, they cannot grow and produce offsprings as fast as frost-intolerant species and are out-competed in frost-free areas [27]. The breadth of tropical climate zone and physiological pressures combined with biotic factors hinder northward wandering and this phenomenon is true for plants and animals (termed Dobzhansky-MacArthur phenomenon) [28]. Animals have to struggle with frost, but they are more mobile and can migrate or become dormant in winter, so this trade-off is not pronounced, but vertebrate and invertebrate fauna almost completely turns over northward and southward moving away from the equator [29]. In addition, many animals’ distribution coincides with that of feeding plants [30].

Many taxonomic groups are of tropical origins, and the main source of diversity is the tropical region (such as birds, amphibians, angiosperms, and many marine invertebrates) [23, 31, 32, 33]. Terrestrial phylogenetical lineages’ expansion is restricted by physiological tolerance toward cold or arid environment, evolution of adaptation is particularly difficult, and these traits have evolved fairly infrequently [34]. Hence, most speciation events occur within the border of biomes to lineages that do not cross boundaries of bioregion. Bacteria do not show particulate biome adherence [35], and criteria that link biodiversity to bioregions are not confirmed; hence, the prevalence of biome crossing lineages, dispersal rates of lineages, and the size of transition zones between biomes should be determined [36]. On the regional scale, speciation is believed to be affected by the population size with the presumption that bigger areas support a larger population [37]. Population size, in turn, is positively related to the physical extent of the bioregion and genetic diversity. Size of distribution area is believed positively correlated with allopatric speciation, and small-ranged species have no opportunity to be divided by a barrier within the range. If ranges are large enough to surround a barrier, the species has also less chance to be divided into two new species. Leading to conclusion that medium-ranged species are predicted to have the highest speciation rate [38]. Bioregions with tectonic activity such as mountain lifting have improved opportunities for speciation and environmental gradient by emerging new mountain ranges. Finally, wide population ranges result in great genetic and phenotypic variability increasing the possibility of survival in a highly heterogenic environment, which is a prerequisite for parapatric speciation [39]. There is a clear correlation between the extent of the area and the likelihood of extinction. In smaller bioregions, the average range of species is also smaller. This is associated with a higher likelihood of extinction due to catastrophic events [40]. In addition, in small populations, both genetic and phenotypic variations are small, which easily leads to inbreeding, and are therefore less able to adapt to changing environmental conditions [41].

The extent and position of the temperate belt have changed many times in the history of the Earth, to which glaciations have contributed [42]. Of course, temperate bioregions have existed for at least 50 million years, where mammals, birds, reptiles, amphibians, and seed plants also lived [43].

The size of the population also positively correlated with the amount of available energy. Of course, in a larger bioregion and in a larger population, this is even more pronounced [44]. This is analogous to the idea of population abundances from metabolic theory, and this assumes that more available energy in one region allows for a larger population size, affecting speciation and extinction rate [45]. High-productivity areas tend to be more heterogeneous, with several sources available to populations, than low-productivity bioregions, increasing the likelihood of speciation [46]. It should be mentioned that energy as a factor influencing speciation rate is not equal to the theory that the total energy available limits the number of species in a given region. Global trends of annual net primary production (NPP) of natural biomes are critical to understanding global (natural and anthropogenic) carbon budgets, and they are essential to understanding the adaptive relationships and the evolution of ecosystems and biomes. The competitive exclusion hypothesis is one of many hypotheses that seek to understand biodiversity dynamics by focusing on primary productivity [47], the energy-richness (or more individuals) hypothesis [48], the integrated evolutionary speed hypothesis [49], and the biological relativity to water-energy dynamics hypothesis [50, 51]. The first of these theories is based on the premise that the prevailing relationship between productivity and species diversity is unimodal (or hump-shaped), while the other three are based on the assumption that the predominant relationship is positive. Another different perspective for explaining the factors that ensure species coexistence is the hypothesis that there is a carrying capacity determined by the energy available. The ecoregions attain equilibrium over time in terms of the number of species and the speciation and extinction are balanced. The addition of a new species to the area causes a decrease in the population size of the previous species, increasing the chance of extinction because there is a limit on the number of individuals for each species. New arrival may lead to extinction of a local species [52]. The ecological needs of different species differ, which concludes that there is more competition between closely related species because they have similar ecological needs. Over time, diversification slows down resulting in a pattern of diversity-dependent diversification [53]. The assumption is that nearby species compete for available resources in a zero-sum game, and the ecological limit determines the maximum number of species within a clade in a region. During the Cenozoic period, when the climate became cooler, speciation also slowed down, as lower average temperatures also lowered net primary production. In the case of a lower net primary production, the number of new species that could theoretically be formed is also smaller [54]. In the case of higher net primary production, more species may develop but a slowdown can be observed here as well, reaching a limit.

A number of phylogenetic studies have reported diversity-dependent species formation, but in many cases due to methodological and sampling problems, in the practice, it has failed to demonstrate that the evolution of new species would slow down after reaching a theoretical limit [55].

Machac and Graham [56], on the other hand, found in their study that the formation of new species does not slow down in the tropical region and that the slowdown may be an artifact and there is no real limit to species formation.

This does not mean that co-occurring species’ biological traits do not impact their diversification rates. Several examples have been reported that how the evolution of new species is influenced by species interactions [57]. However, it is very difficult to detect the persisting and speciation-promoting effect of the area and the source on clade-level properties in lineages and to distinguish it from the diversity-limiting effect of area and productivity [58].

In addition, the theory of ecological limitations did not provide a strong conceptual relation between how the volume of resources is associated with carrying capacity for all organisms, and how resources could then be specifically related to the diversity of species [59]. Large-scale dynamics of species diversity did not correlate well with numbers of organisms, according to previous reviews that found little evidence for the species-energy hypothesis [60]. While new immigration to an area (or new species emerging in situ) would inevitably consume some of the region’s available resources, it is unclear how a new species would affect the community abundances of all other native species unless only one other species exists in the area. The relative abundances of any of these species will differ in an infinite number of ways given a certain amount of resources and a certain degree of species diversity [61]. Furthermore, observational experiments have shown that common organisms in an area may have extraordinarily high relative abundances [62]. If newcomer species decrease the abundance of common species while not reducing the abundance of rarer species, so more rare species can be easily accommodated within the field. Our knowledge of how the relative abundance of species changes over time is complicated by the Milankovitch cycle, which also changes the extent and shape of bioregions in 14, 21, and 100,000-year cycles. These periods are often shorter than we would expect for species formation or extinction [63, 64]. Furthermore, with their recent histories, certain bioregions such as tundra and boreal bioregions are unlikely to have reached equilibrium diversity for trees or vertebrates [65].

Finally, it is unclear which scientific evidence would be required to assess whether bioregions have attained their carrying potential for species diversity. Rather than thinking about whether or not a bioregion represents an equilibrium or nonequilibrium structure, I believe it is more efficient to concentrate on how various drivers can affect speciation and extinction [66].

Species energy, time-integrated area, and tropical conservatism hypotheses are based on some mechanistic assumptions, taking into account population size, speciation, and extinction rates, these are worth combining. These concepts are based on the fact that by observing area and energy over a long period of time, diversity and diversification rates can be estimated on a large scale. Marin et al. [67] concluded that one of the most important factors in predicting species richness is a time-integrated area (area through time). Ecological and climatic stability influences species richness indirectly, altering the evolutionary time (i.e., persistence time) and rate. According to their discovery, global heterogeneity in species richness can be primarily explained by the duration of evolution. Colville et al. [68]. In South Africa, 4813 plant species from Cape Floristic Province and 21 molecularly dated endemic clade were added to the simulation study, and the age and area hypothesis was tested taking into account known climates and topography going back 140,000 years. The regression model showed that long-term stability is the deciding factor in explaining species richness. In general, fossil analyses of both aquatic and terrestrial clades have shown higher rates of speciation (origination) in tropical areas [69, 70]. In the sea, the gradient is less steep because temperatures change less and organisms do not have to adapt to such large fluctuations as on land [71]. The gradient is quite conservative, dispersing events occurring in 4–5% of temperate regions. In most cases, dispersion occurs in other tropical regions. Duchêne and Cardillo [72] came to this conclusion in their study by integrating the phylogeny of 9000 bird species. Dispersal events toward temperate areas are generally no older than the Eocene-Oligocene Climate Transition. Rivadeneira et al. [73] used data from 328 marine mollusk species and 159 genera to explore the evolutionary processes that lead to the emergence of the current observed distribution. To do this, the fossil record, nestedness analysis, and projection matrix are used as complementary approaches. Geographical distribution was nested irrespective of the region of origin of genera, and according to the distribution dynamics model, dispersion events were common from temperate areas to the tropics, where extinction events were much rarer. In conclusion, despite the difficulty of distinguishing the signs of speciation and extinction in phylogenetic studies of diversification, all large-scale phylogenic research papers provide findings that are consistent with the tropical conservatism hypothesis and the area/energy/time hypothesis, namely that species have been concentrated in tropical bioregions to a greater extent than extratropical bioregions. The climate stability hypothesis complements the area/energy/time hypothesis in the sense that it is based on a similar mechanistic basis: the genetic variability of population and the geographical extent and, in return, these factors influence speciation and extinction rates. Building on the projections that a larger area and greater genetic variability can influence species formation and extinction, climate stability postulates that these factors are highly mediated by orbitally enforced range dynamics. Therefore, the time-integrated area of temperate climate regions is likely to fluctuate strongly during cold periods and increase the extinction rate. As the chances of extinction increase due to minimum temperatures, a cumulative time-integrated area may not be the best way to test the relationship between species richness and total area available for populations within a region. Instead, if contraction has resulted in extinction events, it is worth working with the minimum area when determining the species richness. Paleoclimatic changes during the Paleo and Neogene allowed or hindered species wandering between areas, as well as regional extinctions, leaving a mark on species and genera distribution. Few species and genera are disjunct between eastern North America and East Asia among temperate plants, suggesting past connectivity over the Bering land bridge as well as climate-driven extinctions from Europe and western North America [74]. Quaternary glacial-interglacial oscillations have left legacies in existing species ranges, according to a wide body of evidence. Ordonez and Svenning [75] examined the distribution patterns of Europe’s contemporary vegetation using six independent lineages (Caryophyllales, Brassicales, Ranunculales, Saxifragales, Rosales, and Malpighiales). The Pleistocene climate, the former location and extent of refugium, the accessibility of areas after the Ice Age, and the contemporary environment play a major role in their current distribution. In concordance with a previous study, Costa et al. [76] concluded that climate stability played key role in Holocene biodiversity of the Amazonian-basin using 30 kyr pollen record and random forest classification. Decreases or fluctuations in temperature negatively correlate with species richness [77]. Deep-sea invertebrates are exception to the role because they do not exhibit equator-pole diversity gradient. Marine invertebrates can be much more diverse in deep waters, which are always roughly 4°C, than in shallow seas. But even in this case, stability is very important. So, constant temperature and access to resources have no variance over time. Deep sea is not productive at all, but resource availability is constant throughout the year [78]. A study of the last 500 million years shows that a steep gradient exists only in the last 30 million years due to cooling. During warm periods, the gradient was much shallower or it was turned around, and there were times when the temperate zone had maximum biodiversity. At that time, the climate was much more stable throughout the world, with few fluctuations [79]. High temperatures have direct positive effect on ectothermic animals, as physiological processes accelerate and evolutional processes can be faster. Faster metabolism leads to shorter generational times, which, together with a higher mutation rate, leads to the formation of new species [80].

Due to the impact of temperature on fostering reproductive isolation, the evolutionary pace hypothesis suggests that speciation rate may be higher in warmer bioregions. Orton et al. [49] conducted a comprehensive study involving multiple phyla (Arthropoda, Chordata, Mollusca, Annelida, Echinodermata, and Cnidaria), COI (Cytochrome c Oxidase subunit I) sequences, and 8037 lineages, but only 51.6% of pairs exhibit higher mutation rate near the equator. For the remainder, the mutation rate was higher in the higher latitudes. This is the most comprehensive study in the literature that has occurred in recent years, and although the result has proved significant, the results are not entirely conclusive to prove evolutionary speed hypothesis.

3. Biotic factors

Organisms also interact with one another, and the effect on one another other also influences evolution. Andresen et al. [81] proved relationships are stronger and more diverse than in the temperate zone. Four different hypotheses attempt to explain species richness: Two involve the speciation (enemy-mediated habitat and the geographic mosaic of coevolution) and two relate to the existence and retention of diversity (competition causing finer niches and predation promoting coexistence). If access to resources differs in two different habitats, the plant will find it more difficult to regenerate the damage caused by herbivores and parasites in places where nutrients are less accessible. Therefore, they need to produce several compounds that keep animals away. However, due to protection, they grow more slowly and are less competitive with specimens living in nutrient-rich areas [82]. Because there are more enemies in productive environments in the tropics, this effect is also stronger. During the formation of the new species, it specializes in a particular habitat with growth protection optimization [83]. Different selection and speciation probabilities between interdepending mutualist or antagonistic species, in tropical climates, should be higher. Organisms are rarely killed by abiotic stress in tropical climates, with most of the selection processes in the tropics controlled by biotic factors. These factors evolve themselves and give an impetus to the evolution of the other species. In tropical environments, where seasonal differences are small, there are several interacting species (plants, herbivores, pathogens, predators, mutualists, etc.) and their relationships persist throughout the year. In cold climates, seasonality disrupts relations, slowing down co-evolution. In stable warm environments, co-evolution is faster and easier to develop mutualistic interrelationships [84]. The novel protection mechanism protects the plant from enemies, which enables the plant to increase its range, stimulating allopatric specificity. But if this enemy is able to adapt to the defense mechanism, then the range of the plant may shrink. Similarly, specialization may lead to speciation through the development of the host race or the increase in patches of geographical specialists that lead to differentiation. These processes will also increase over time and generate a positive feedback loop [85]. An example is the relationship between butterflies in the Nymphalidae family and solanaceae feed plants. The Solanaceae family separated from its sister groups 49−68 million years ago and then diversified (29–47 MYA). Around this time, the Ithomiini subfamily of the Nymphalidae family was also formed and diversified [86]. But there are also examples where this diversification effect has not been confirmed. According to Kaczvinsky and Hardy [87], the emergence of a new plant-predator relationship could increase the chances of extinction. The development of a connection with the new plant can be due to the significant fitness reduction of ancient feed plant. This can be caused by several factors, such as increasing competition for diminishing resources, the development of a new defense mechanism, the emergence of a new invasive species, and the emergence of new natural enemies. If a change in the feeding plant of an insect is caused by such an effect, it will cause a decrease in the population size and chance of speciation. With decreased overall performance of ancestral host and presumably minimal overall performance of new host, the growth rates and adequate sizes of herbivorous insect populations should shrink, as well as their geographic and climatic area.

Two other hypotheses explain that in areas where interrelationships between organisms are stronger, the width of the niche is smaller, in the sense that it uses habitat and resources. As competition intensifies, niches can split up, resulting in a finer niche for evolving new species. Thus, the existence of more species can be imagined within the community [22]. Harmáčková et al. [88] tested the hypothesis by using 298 Australian songbirds’ (Passeriformes) data. It was expected that the species richness-specialization relationship is stronger in particularly species-rich communities, where annual precipitation is high and vegetation is complex. They also tested the extent of niche overlap. A positive relationship was found between specialization and species richness, but the direction and strength of relationship vary according to traits and area size. The specialization-species richness relationship is clear only in the forage stratum and has increased toward a smaller area only for habitat and diet. At the same time, local communities had a high overlap in habitat and diet. In a particularly species-rich community, no particularly strong link was found between species richness and specialization. However, they found a negative connection between specialization and overlap, meaning that species separate the ecological space on the basis of where food is found. These just weakly supported their expectations. The specialization in forage stratum has probably been significant in promoting species coexistence. On the other hand, while several species were habitat and diet specialists, high overlap in these traits did not rule out coexistence. The stronger predator (or herbivore) is able to drive selection in the antipredator traits in the prey (or plant). This is the basis of predator-victim specialization, the prey (or plant) can compete for a predator-free environment, leading to greater coexistence of the prey (or plant) species. Horst and Venable [89] studied the seed predation of rodents in the Sonora Desert. The rodents prefer the seeds of a certain species out of three different plants, which allows the two other plants to coexist. Regular predation on the more common species reduces interspecific competition between the three plants.

Phylogenetic studies of trees, birds, mammals, reptiles, and amphibians show that tropical regions are the source of biodiversity, composed of both ancient and recently evolved lineages. Moderate regions contain only a fraction of this. Over the past millions of years, the climate of tropical areas has been more stable, which has helped new species to evolve and reduced extinction rate. And niche conservatism has prevented lineages to wander to the temperate zone. It seems that the energy available is a secondary factor because deep sea life has become almost completely independent of it. But temperature and availability of resources are stable there in the long run. The time-integrated area is the most important controller of evolutionary processes. The seasonality of temperature and productivity affects the number of resources available on land, which determines the size of the populations. And lastly, speciation and coexistence are augmented by biotic interactions.