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3.19: Speciation and extinction - Biology

3.19: Speciation and extinction - Biology


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As we have noted, an important observation that any useful biological theory needs to explain is why there are so many (millions) of different types of organisms currently present on Earth. What leads to the formation of a new species or the disappearance of existing ones?

The concept of an organism’s ecological niche, which is the result of its past evolutionary history (the past selection pressures acting within a particular environment) and its current behavior, combines all of these factors. In a stable environment, and a large enough population, reproductive success will reflect how organisms survive and exploit their ecological niche. Over time, stabilizing selection will tend to optimize the organism’s adaptation to its niche. At the same time, it is possible that different types of organisms will compete for similar resources. This interspecies competition leads to a new form of selective pressure. If individuals of one population can exploit a different set of resources or the same resources differently, these organisms can minimize competition with other species and become more reproductively successful compared to individuals that continue to compete directly with other species. This can lead to a number of outcomes. In one case, one species becomes much better than others at occupying a particular niche, driving the others to extinction. Alternatively, one species may find a way to occupy a new or related niche, and within that particular niche, it can more effectively compete, so that the two species come to occupy distinct niches. Finally, one of the species may be unable to reproduce successfully in the presence of the other and become (at least) locally extinct. These scenarios are captured in what is known as the competitive exclusion principle or Gause's Law, which states that two species cannot (stably) occupy the same ecological niche - over time either one will leave (or rather be forced out) of the niche, or will evolve to fill a different (often subtly) niche. What is sometimes hard to appreciate is how specific a viable ecological niche can be. For example, consider the situation described by the evolutionary biologist Theodosius Dobzhansky (1900-1975):

Some organisms are amazingly specialized. Perhaps the narrowest ecologic niche of all is that of a species of the fungus family Laboulbeniaceae, which grows exclusively on the rear portion of the elytra (the wing cover) of the beetle Aphenops cronei, which is found only in some limestone caves in southern France. Larvae of the fly Psilopa petrolei develop in seepages of crude oil in California oilfields; as far as is known they occur nowhere else.

While it is tempting to think of ecological niches in broad terms, the fact is that subtle environmental differences can favor specific traits and specific organisms. If an organism’s range is large enough and each individual’s range is limited, distinct traits can be prominent in different regions of the species’ range. These different subpopulations (sometimes termed subspecies or races) reflect local adaptations. For example, it is thought that human populations migrating out of the equatorial regions of Africa were subject to selection based on exposure to sunlight in part through the role of sunlight in the synthesis of vitamin D.97 In their original ecological niche, the ancestors of humans were thought to hunt in the open savannah (rather than within forests), and so developed adaptations to control their body temperature - human nakedness is thought to be one such adaptation (although there may be aspects of sexual selection involved as well, discussed in the next chapter). Yet, the absence of a thick coat of hair also allowed direct exposure to the UV-light from the sun. While UV exposure is critical for the synthesis of vitamin D, too much exposure can lead to skin cancer. Dark skin pigmentation is thought to be an adaptive compromise. As human populations moved away from the equator, the dangers of UV exposure decreased while the need for vitamin D production remained. Under such condition, allelic variation that favored lighter skin pigmentation (but retaining the ability to tan, at least to some extent) appears to have been selected. Genetic analyses of different populations have begun to reveal exactly which mutations, and the alleles they produced, occurred in different human populations as they migrated out of Africa. Of course, with humans the situation has an added level of complexity. For example, the human trait of wearing clothing certainly impacts the pressure of “solar selection.”

A number of variations can occur over the range of a species. Differences in climatic conditions, pathogens, predators, and prey can all lead to local adaptations, like those associated with human skin color. For example, many species are not continuously fertile and only mate at specific times of the day or year. When the range of a species is large, organisms in geographically and climatically distinct regions may mate at somewhat different times. As long as there is sufficient migration of organisms between regions and the organisms continue to be able to interbreed and to produce fertile offspring, the population remains one species.


Extinction

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Extinction, in biology, the dying out or extermination of a species. Extinction occurs when species are diminished because of environmental forces (habitat fragmentation, global change, natural disaster, overexploitation of species for human use) or because of evolutionary changes in their members (genetic inbreeding, poor reproduction, decline in population numbers).

Rates of extinction vary widely. For example, during the last 100,000 years of the Pleistocene Epoch (about 2.6 million to 11,700 years ago), some 40 percent of the existing genera of large mammals in Africa and more than 70 percent in North America, South America, and Australia went extinct. Ecologists estimate that the present-day extinction rate is 1,000 to 10,000 times the background extinction rate (between one and five species per year) because of deforestation, habitat loss, overhunting, pollution, climate change, and other human activities—the sum total of which will likely result in the loss of between 30 and 50 percent of extant species by the middle of the 21st century.


Background

A key recurring question in evolutionary biology is what evolutionary novelties lead to shifts in speciation and/or extinction rates. Historically, the fossil record has been used to address this question. More recently, developments in phylogenetic comparative methods present an alternative to use for groups that have poor to nonexistent fossil records [1]. Among these developments are probabilistic models that enable researchers to infer both the evolution of the character traits responsible for diversification patterns as well as the diversification rates themselves [2, 3]. Phylogenetic comparative methods have now been directed at a variety of different taxonomic groups (e.g. flowering plants [4] mammals [5] birds [6]).

A limitation of phylogenetic methods is that phylogenetic trees represent only the ancestors of termini represented in the phylogeny. Reconstructing the richness of unsampled subclades is extremely difficult. An important assumption of many phylogenetic methods is that they require ultrametric trees and thus require all termini to represent extant taxa, with the result that extinct lineages within a study group are necessarily left unsampled and so become problematic [7,8,9]. In theory, entirely neontological datasets could be used to reconstruct histories of declining clades because the likelihood functions for net-negative diversification rates are well-defined. However, neontological studies from real clades that are in decline often fail to identify the net-negative diversification rates these lineages experienced in the past [8]. Many extant groups were more diverse in the past, including lineages of invertebrates (e.g. brachiopods, bryozoans, crinoids [10]), vertebrates (gar fish, crurotarsans, hominids [11]), and plants (lycopods, cupressaceous conifers, gnetophytes, sycamores [12]). The ubiquity of declining lineages suggests that such decline is a general behavior of clades, with diversifying lineages merely having yet to reach the declining phase of their history [13].

Multiple studies have examined the effects that changing diversification rates have on the usefulness of phylogenetic comparative methods in reconstructing relationships between state transitions and diversification [14, 15]. Some neontological approaches enable use of phylogenetic methods that account for some of these effects (e.g. [16] for successively-diversifying subclades, [17] for density-dependent diversification). Here we examine mechanisms that limit the usefulness of phylogenetic methods to correctly infer relationships between the character states and diversification.

In this study, we set out to address three questions concerning the behavior of the binary state speciation and extinction (BiSSE) method [2], the simplest of a family of similar (SSE) methods that use a likelihood optimization routine to compare models of speciation, extinction, and state transition given a phylogenetic tree of extant taxa. Here we use BiSSE to analyze a single character with two possible states, with speciation and extinction rates associated with each state. Although SSE methods account for diversification rate shifts as a result of changes between the character states, persistently declining diversification rates still violate the assumptions of all SSE methods. Our three questions are as follows: (1) how severely must BiSSE’s assumptions of constant speciation and extinction rates be violated before it fails to be useful when modeling the effects of the character states on diversification parameters? Under the condition where the character states have no effect on speciation rate we predicted the most likely BiSSE models would be those with higher rates of speciation in a clade’s ancestral state. This is because the frequency of a character’s ancestral state must necessarily be high early in a clade’s history, since the derived state has not had a chance to evolve yet. By the time the derived state has become common, speciation rate has declined. For this reason, the most likely BiSSE model would have the derived state associated with the decline in speciation rates, even though it is not. (2) Is BiSSE’s power to detect biases in transition rates between the character states compromised if characters evolve in a punctuated fashion (sensu [18] see also ClaSSE, [19])? We predicted that a punctuated equilibrium simulation would result in the best BiSSE model featuring the derived state having a lower rate of reversion to the ancestral state than vice-versa. The rationale is that an asymmetry in favor of the ancestral state transitioning to the derived state reflects events early in clade history when the ancestral state is common and the clade is diversifying rapidly. (3) Do decaying, constant, or increasing extinction rates also affect how useful BiSSE is for recovering speciation rate? Using reasoning similar to the first question we predicted that decreasing extinction rates associated with both character states would result in the most likely BiSSE model having the ancestral state associated with higher extinction rates.


Adaptation, speciation and extinction in the Anthropocene

Humans have dramatically altered the planet over the course of a century, from the acidity of our oceans to the fragmentation of our landscapes and the temperature of our climate. Species find themselves in novel environments, within communities assembled from never before encountered mixtures of invasives and natives. The speed with which the biotic and abiotic environment of species has changed has already altered the evolutionary trajectory of species, a trend that promises to escalate. In this article, I reflect upon this altered course of evolution. Human activities have reshaped selection pressures, favouring individuals that better survive in our built landscapes, that avoid our hunting and fishing, and that best tolerate the species that we have introduced. Human-altered selection pressures have also modified how organisms live and move through the landscape, and even the nature of reproduction and genome structure. Humans are also shaping selection pressures at the species level, and I discuss how species traits are affecting both extinction and speciation rates in the Anthropocene.

1. A human-modified world

The human population has grown from 1.8 billion a century ago to 7.6 billion today (averaging approx. 1% increase per annum [1,2]). Population growth tells only part of the story. Alongside demographic growth, the ecological impacts per person have risen. Venter et al. estimated the per capita growth in human footprint on the landscape at approximately 0.52% per year (from 1993 to 2009) [3]. The product of the two—population size and per capita demand—has thus grown exponentially faster than either on its own.

The burgeoning demand on the resources of the planet has altered three-quarters of Earth's ice-free surface [4]. Timber and other resource extraction, agricultural expansion and an increasing incidence of fire have reduced the intact forested landscape at a rate of 0.57% per year [5]. Harvesting has caused the global biomass of predatory fish to decline by two-thirds over the last century [6]. Human land use has led to an estimated loss of 10 14 kilograms of organic carbon from the Earth's topsoil (approx. 8% of the top 2 m of used land), reducing productivity and contributing to CO2 emissions [7]. One-quarter of the terrestrial surface is now considered degraded due to the combined effects of erosion, pollution, compaction and salinization [8]. Over the past century, temperatures have increased by 0.85°C, sea levels have risen by 0.2 m, and oceans have become 26% more acidic due to anthropogenic climate change [9]. The resulting pressures on natural populations have caused a 60% decline in the population size of vertebrate wildlife between 1970 and 2014, based on a meta-analysis of long-term data from 4005 species [10]. The global scale of geochemical, climatological and biological changes caused by humans has led scientists to propose a new epoch, the Anthropocene, to signify the stratigraphically distinct and pervasive impact of humans on the planet [11].

Beyond the numbers, the world's biological diversity is changing, through evolutionary change at both the within and between species levels. In this essay, I reflect upon the myriad impacts that humans have had on evolution. The nature of selection faced by species across the planet has changed, as organisms are favoured that best tolerate the land development, harvesting, species introductions and environmental changes caused by humans. Species are at a greater risk of extinction than pre-human levels, causing selection at the species level due to the loss of species that are large-bodied, specialist or otherwise vulnerable to human activities. Although less well understood, humans have also altered the processes that lead to the formation of new species, and again this impact is not affecting all of the world's species equally. I argue that humans have altered the course of evolution to a degree that is unprecedented for a single species in a single century and close by discussing why this matters.

2. Anthropogenic selection pressures

In the first two chapters of The Origin of Species, Charles Darwin contrasted selection upon variation under domestication and under nature. The distinction is becoming increasingly blurred, with humans selecting for variants across all species that best tolerate the environmental conditions that we impose. Here, I discuss several unintended selection pressures that are altering the evolutionary trajectory of life on Earth (intended selection pressures, e.g. through antibiotic application or selective breeding, are not discussed). My goal is not to give an exhaustive list, but to highlight the range, potency and idiosyncrasy of selection pressures induced by humans (figure 1 see also [19] and references therein).

Figure 1. Human-altered selective forces. (a) Selection in built environments: feathers left on a window illustrate the high death toll of birds colliding with buildings and automobiles [12], selecting against migratory behaviour [13] and for manoeuvrability [14]. (b) Selection to avoid hunting or harvesting: humans target individuals with preferred traits, selecting against traits such as long ivory tusks [15]. (c) Selection in novel communities: both abiotic and biotic selection pressures are reshaped when humans bring together species in new assemblages, as found in cardinals nesting in introduced honeysuckles [16]. (d) Selection on dispersal: fragmented landscapes select for individuals that can remain in hospitable environments, favouring non-dispersing seeds in Crepis sancta [17]. (e) Selection on inheritance systems: rapid evolution associated with human cultivation can alter the genome, with increased recombination rates and polyploidy found in many domesticated plants, such as oats [18]. Photographs: (a) Alan Hensel (b) Sarah Otto (c) Jeff Whitlock (d) Susan Lambrecht (e) Henrik Sendelbach.

(a) Selection to survive in built landscapes

While urban areas and similarly artificial human-dominated landscapes only comprise approximately 1% of Earth's surface [8,20], the selective pressures induced in cities and other built landscapes are often intense and multifarious [21]. Building strikes and domesticated cat predation are now major mortality sources for birds and other flying animals, with tallies of 800 million collision deaths and 2.4 billion cat predation events annually in the USA [12]. Such high mortality levels can induce strong selection pressure to alter behaviour (e.g. flying speed, perch height), morphology (e.g. wing shape) and life-history strategies (e.g. age at first reproduction). While not fully documented, the evidence is accumulating for widespread evolutionary responses to these selection pressures. For example, the proportion of sedentary individuals within great bustard (Otis tarda) populations increased from 17% to 45% over a 15-year period, with collisions being the major source of death for migrating individuals [13]. The wing span of cliff swallows has evolved to be shorter near roads, with road-killed swallows having longer wings, consistent with selection for increased manoeuverability in the face of traffic [14].

While urban evolution has received less attention than urban ecology, cities are increasingly recognized as highly altered selective landscapes, providing the opportunity to study evolutionary shifts that occur in a replicated fashion across cities [20]. For example, mosquitoes of the molestus form of Culex pipiens have repeatedly taken advantage of the increasing availability of subways and other urban underground areas with readily available human hosts to transition to an underground life history [22] the evolution of biting preferences for humans over birds has concomitantly evolved independently in Europe [23] and North America [24]. Urban bird feeders provide an artificial food subsidy, selecting for shifts in beak size and bite forces in urban house finches (Carpodacus mexicanus), with correlated changes in bird song [25]. White clover (Trifolium repens L.) has evolved greater tolerance to freezing within three of four northeastern North America cities, a response ascribed to the higher incidence of freeze–thaw cycles within the urban environment compared to surrounding non-urban areas [26]. The altered thermal environment of cities has also been invoked to explain shifts in migratory behaviour in urban blackbirds, which are more sedentary than paired rural populations [27].

Even the presence of human activity can induce fear and behavioural shifts in wildlife. In a meta-analysis of 72 studies, Gaynor et al. showed a 36% increase in nocturnality among mammals, essentially a human-avoidance mechanism, with an even stronger effect in cities, but whether genetic changes have occurred causing (or responding to) this shift towards nocturnality is unknown [28]. In other cases, genetic differences underlying behavioural shifts in response to humans have been implicated. For example, a study of black swans (Cygnus atratus) found that more wary individuals avoided cities and differed genetically at a dopamine receptor gene associated with fear in animals (DRD4), compared to more human-tolerant urban swans [29].

(b) Selection to avoid hunting or harvesting

Humans typically hunt or harvest in a selective manner, leading to ‘unnatural selection’ in the terminology of Allendorf & Hard [30], which often drives traits in exactly the opposite direction preferred by humans. Hunting pressures have long been studied for the selective pressures induced, including an early analysis by Haldane [31] documenting the decline in foxes of the silver coat variant, which was highly prized by trappers. From reductions in tusk size among elephants [15] to horn size among bighorn sheep [32], hunting selects for those traits that keep animals out of the cross-hairs [30].

Fishing also induces selection pressure on body size, life history and morphology often in a manner that makes fish less catchable and/or less desirable. In an analysis of 143 time series, Sharpe & Hendry found rapid decreases in fish length at 50% maturity and earlier maturation, changes that were strongly correlated with the intensity of fishing pressures [33]. Fishing not only selects on size but also shape and behaviour. For example, recreational hook-and-line fishing has selected for smaller mouth gapes [34], while gillnet fishing has selected against a more active, bold and aggressive genotype in rainbow trout [35]. These evolutionary responses generally reduce catch value per unit effort.

Across a broad spectrum of harvested species, rates of evolutionary change induced by human culling were found to be three times higher than in natural systems [36]. Reflecting upon harvesting in general, Sharpe & Hendry [33] concluded that ‘exploitation is a very strong selective force, probably outside the normal intensities of selection in most natural populations’.

(c) Selection in novel communities

Beyond altering the physical environment, humans are altering the biotic environment faced by species across the planet. Most obviously, communities are altered through the introduction of non-native species but also when species' ranges shift at different rates in response to anthropogenic habitat alteration and climate change. Bumblebees in North America and Europe, for example, are not spreading poleward in response to warming at their northern range edges as much as expected based on contractions at their southern range edges [37]. Thus, plants whose ranges are shifting poleward will probably face different communities of pollinators.

When humans bring species together into novel assemblages, strong evolutionary and co-evolutionary selective pressures can result, especially if the species within a new community had little to no prior contact. Strauss et al. [38] reviewed 31 well-documented cases of altered evolutionary responses to introduced species, including insects evolving in response to novel host plants, plants evolving in response to novel herbivores, fish evolving in response to novel competitors and predators, and resistance evolving in response to novel diseases. Responses involved morphological and/or physiological changes (21 cases), behavioural changes (11 cases) and life-history changes (3 cases). As a striking example, cardinals in high condition (as indicated by bright red coloration) prefer to establish territories within an introduced honeysuckle, where their nests are more heavily predated the net result is a reversal in the direction of selection for bright plumage [16]. Altogether, these diverse examples illustrate the variety of ways that humans indirectly alter selection by changing the biological community within which species live and reproduce. Metaphorically, the Red Queen must run faster and in new directions to keep her place within newly assembled communities.

Beyond altered biotic selection pressures, changes to the community can affect how species respond to abiotic changes in their environment. In Kleynhans et al. [39], we found that the grass Poa pratensis evolved increased fitness in response to 14 years of elevated CO2 supplementation in the field, but only when plants remained in the same community context in which selection had occurred. Our results suggest that the realized selection pressures induced by anthropogenic environmental changes are reshaped by the surrounding community (essentially altering the direction and magnitude of selection experienced in multivariate trait space). Consequently, adaptation to abiotic changes, such as elevated CO2, may be quite sensitive to variation over time and space in the surrounding community.

(d) Selection on dispersal

While the above examples focused on trait responses to selection, human-induced selection pressures can also shape how species live and move through their environment. In increasingly fragmented and exploited landscapes, dispersal and migratory behaviour are subject to different selection pressures in the Anthropocene.

Theoretically, we expect reduced dispersal rates to evolve within fragmented but stable patches so that organisms can remain in hospitable environments [40]. For example, we found that selection to avoid fishing pressures is expected to select for fish that remain in marine protected areas, potentially improving the efficacy of marine reserves over the span of decades [41]. Empirically, selection against dispersal has favoured heavy non-dispersing seeds relative to lighter dispersing seeds of the weedy hawksbeard (Crepis sancta) in Montpellier, France, where the soil is patchily distributed among the built environment [17]. Similar changes in dispersal propensity and distances moved have been observed in several systems (see citations in [42]).

While reduced dispersal protects local populations in the short term, dispersal is critical over the long term for recolonizing patches after local extinction events and for facilitating genetic exchange and the maintenance of variation. With increasing patch extinction rates, theory predicts that higher dispersal rates can be favoured, allowing faster recolonization [43]. Consistent with these expectations, a greenhouse experiment with Arabidopsis thaliana found that plants evolved to disperse three times farther across fragmented habitats in only six generations [44]. Yet increasing dispersal through unsuitable habitats is risky. To reduce these risks, selection can favour dispersal behaviours that are more leptokurtic (either staying put or dispersing far) or more targeted to suitable habitats [42]. A study of the butterfly Proclossiana eunomia in Belgium found, indeed, that individuals were more likely to stay within their natal patch in the most fragmented of the landscapes studied, were more likely to die if they dispersed, but when they dispersed they flew faster and straighter through inhospitable habitats [45,46], although the extent to which this represents a recently evolved trait is uncertain.

With climate warming, the availability of resources in the spring is shifting earlier in many parts of the world, with the timing of migration moving forward by an estimated 2.3 days per decade [47]. Although the mechanisms are often unknown, evidence for at least some genetic response to selection is mounting. For example, a study of pink salmon in Alaska found that migration back into streams occurred two weeks earlier than 40 years ago, accompanied by a three-fold decrease in a genetic marker associated with late dispersal [48].

Migratory behaviour can also be affected by anthropogenic shifts in resource availability. The popularity of bird feeders and a warming climate has made for more hospitable winters for birds in Britain over the past century [49]. In response, a sub-population of blackcap warblers (Sylvia atricapilla) has evolved a new migratory route to Britain, with offspring raised in captivity showing different flight orientation preferences than related birds that migrate to Spain [50].

Successful dispersal also requires successful breeding in a new environment. As a consequence, we may expect features that enhance reproductive assurance, include selfing, asexuality and perenniality, to evolve when novel sites are being colonized (Baker's rule [51]). Indeed, some annual plants are more self-compatible in their invasive range than where they are native (Echium plantagineum) and where weedy than non-weedy (Centaurea solstitialis) [52].

(e) Selection on inheritance systems

The very nature of inheritance can also be shaped by human-altered selection pressures. During periods of rapid environmental change, selection favours increased mutation rates, particularly within clonal organisms where mutator alleles can hitchhike along with the beneficial mutations that they generate. Mutator strains are repeatedly observed in microbes following exposure to antibiotics but also in response to selection on virulence and transmissibility (see [53] for examples).

To reduce selective interference among loci, the rates of sexual reproduction and recombination are also expected to rise following periods of intense selection. Evidence for the impact of humans on recombination rates has been found in both domesticated mammals (see triangles in fig. 1 of [54]) and plants [18].

Plants living in human-disturbed habitats were found to inbreed more than in undisturbed habitats, altering patterns of inheritance in many species [55]. In their review, Eckert et al. [55] attribute this rise in inbreeding to pollen becoming more limited in disturbed areas, due to either a reduced abundance of pollinators and/or a lower density of plants. While these shifts in the mating system cause genetic changes (e.g. higher homozygosity), how they alter selective pressures is not yet known. Eckert et al. provide several predictions for how selection probably shifts in response to pollen limitation, calling for empirical work linking human disturbance to floral and mating system evolution.

Genome size has also been inadvertently shaped by human selective pressures. In many crop species, genome doubling (polyploidization) has an effect on agriculturally valuable traits, such as fruit size, with humans selecting and propagating polyploid varieties of many crops (e.g. blueberries, wheat, sugar cane, coffee and cotton [56]). Structural changes in the genome, including gene loss/duplication and chromosomal loss/duplication, also represent one of the fastest routes by which organisms adapt to an altered environment. In an experiment with yeast adapting to high copper concentrations [57], which is often used in wine grape cultivation, we found both gene duplications and aneuploidy arose repeatedly and rapidly (in the course of two weeks) [57]. Similarly, Gallone et al. [58] found ‘staggering’ levels of copy number variants and genomic structural changes in domesticated strains of yeast used in brewing.

While not exhaustive, these examples highlight the dramatic ways in which human-imposed selection pressures are altering organisms, down to the very way that they reproduce their genomes.

4. Extinction in the Anthropocene

In addition to altering the selective forces shaping evolution within species, humans are also imposing selection at the species level. Most alarmingly, humans have increased the rate at which species are going extinct and strongly determine which species are at risk of extinction.

Pre-humans, the background rate of extinction, estimated from lineage-over-time plots, is 1000 times lower than in the Anthropocene [59]. Over one in five species of vertebrates [60], invertebrates [61] and plants [62] are now at risk of extinction. While currently a minor risk factor, continued climate change is projected to rival habitat loss as the primary threat to species at risk by the end of this century [63].

Extinction in the Anthropocene is non-random, which generates species-level selection against those traits that elevate extinction risk. Many of the known extinctions over the past two centuries have been caused by overexploitation, with humans hunting to extinction species such as the sea mink, Caribbean monk seal, great auk and passenger pigeon. Such extinctions permanently remove species prized by humans (e.g. for the fur of the monk seal) and whose traits make them particularly susceptible to harvest (such as the flocking behaviour of the passenger pigeon). Large body size has also increased extinction rates of species subject to hunting throughout the past 50 000 years, eliminating half of the large terrestrial mammalian species [64].

Extinction driven by overexploitation tends to be noticed. Humans pay attention to species that they hunt and fish, documenting their demise. Extinction from overexploitation can also be rapid, with per capita mortality remaining high even as the targeted population decreases in size if humans search farther and innovate to continue to capture the resource (e.g. [65]). An accelerating approach to extinction or ‘extinction vortex’ can even result if rarity increases the value of the exploited species to humans [66].

By contrast, many of the unknown extinctions from the past two centuries, as well as current extinction threats [64], are caused by habitat loss and degradation. Unlike overexploitation, extinction caused by habitat change can be a prolonged process [67], with at-risk species persisting in remaining patches of suitable habitat. Indeed, a decelerating approach to extinction is expected if habitat most desirable to humans is converted first, leaving remnant patches that are protected, hard to access or difficult to develop where species can persist.

While species with patchy ranges may persist over the short term, they are subject to declining genetic diversity and localized ecological disasters that place them at risk of extinction in the long term. As a consequence, anthropogenic habitat change is thought to have generated a substantial extinction debt (e.g. [67,68]), which may take years to millennia to realize, depending on the extent of habitat loss [67]. The extinction debt, along with the fact that anthropogenic habitat change endangers many rare species that are unknown to science [69], makes it challenging to document fully which species are going extinct and what traits are being lost.

By examining which types of taxa are most endangered, however, studies have shown that the extinction debt is not borne evenly among species. Species with small ranges are particularly threatened [69]. By contrast, widespread species, generalists, dispersive species and human commensals are, on average, less prone to extinction [70]. Other less obvious character traits have also been shown to be associated with an increased threat of extinction. By comparing the IUCN red-list status of species, Vamosi & Vamosi [71] found that plants with separate sexes (dioecy) are more likely to be at risk of extinction than hermaphroditic sister clades, potentially because pollen flow and seed dispersal are more easily disrupted when male and female functions reside in different plants. Woody plants [71] and tropical plants [72] are also more at risk. In birds, species with larger body sizes [73], lower fecundity [73] and larger testes size (an indicator of stronger post-mating sexual selection) [74] are more likely to be endangered, potentially because such species are less able to recover when driven to small population sizes.

Humans are thus reshaping the living world through non-random extinction, leading to a rise in frequency of widespread species that tolerate human activities, a fragmented environment, and an altered climate.

5. Speciation in the Anthropocene

Relative to extinction, less is known about how humans have altered the rate of speciation. Estimates of background speciation rates can also be estimated from lineage-over-time plots and from intervals between nodes in a phylogeny (especially nearer the present), suggesting that species' splits occur at roughly every 2 Myr, on average, per lineage [75]. Estimating modern speciation rates is more challenging. It is easier to document the loss of a species previously known to be present than to witness the birth of a species, especially when divergence is so recent that few characters distinguish the new species from its parent(s), leading to cryptic young taxa [76].

While the effect of humans on the rate of speciation is unknown, many examples exist of how humans have altered the speciation process [77]. The mechanisms underlying these impacts can be roughly categorized as human-altered niches, human-altered contact and human-altered selection.

(a) Human-altered niches

Human activities have altered and created novel niche space. Crop domestication and the spread of agriculture, in particular, have generated novel plant hosts for many insects and pathogens. One of the best documented cases of contemporary speciation is Rhagoletis pomonella, following a host switch to domesticated apples [78]. Similarly, the introduction of invasive honeysuckle (Lonicera) from Asia provided a novel niche that favoured the spread of a newly formed homoploid hybrid species of Rhagoletis (between R. mendax and R. zephyria) [79]. Host specialization onto different crops has also driven speciation in fungi, with Rhynchosporium, for example, diversifying into at least three pathogenic species specialized on different cereals in the past 4000 years [80].

Contaminated sites, e.g. mine tailings, can also promote speciation because of the strong ecological selection for locally adapted genotypes. For example, the sweet vernal grass, Anthoxanthum odoratum L. has adapted to heavy metals surrounding a mine active in the mid- to late 1800s. This local adaptation has been accompanied by a shift in flowering time and an increase in selfing rate, generating substantial reproductive isolation that has been maintained over the past 40 years [81]. Adaptation to copper-heavy mine tailings has also driven both local adaptation and reproductive isolation in Mimulus gutatus [82].

Climate change is also opening up niches in locations that previously were inaccessible. The blackcap warblers that now migrate to the UK are beginning to show evidence of assortative mating and genetic differentiation from those that migrate to Spain [83], exhibiting the initial steps of speciation in under a century.

Humans are, however, also homogenizing environments that previously were heterogeneous, eroding the potential for speciation. For example, the nesting habitats of benthic and limnetic sticklebacks in Enos Lake in western Canada were homogenized after the invasion of signal crayfish in the 1980s. As a consequence, the two young stickleback species collapsed into a single hybrid swarm [84]. Similarly, the narrowing of the visual environment in Lake Victoria due to human-caused eutrophication has led to the loss of mate preferences that maintain species, with a fourfold reduction in the number of species in the most turbid waters [85].

(b) Human-altered contact

The global mixing of species by either intentional or accidental introduction by humans is also providing novel opportunities for speciation. In particular, hybrid speciation is facilitated between species that were previously isolated. A prime example is the grass Spartina alterniflora, native to eastern North America and introduced by humans both to western North America and Europe [86]. Hybridization with native S. foliosa in California has led to a hybrid swarm, while hybridization with S. maritima in France and separately in England generated sterile hybrids (Spartina × neyrautii and S. × townsendii, respectively). Polyploidization of S. × townsendii subsequently produced Spartina anglica, a fertile and highly invasive species that vigourously colonizes and alters sedimentation in salt marshes [86].

Spartina illustrates the opposing effects that human introductions are likely to have on speciation. On the one hand, species brought into secondary contact by humans can collapse into a hybrid swarm when reproductive isolation is not sufficiently strong (as in western North America [86]), hindering speciation. On the other hand, crosses between more isolated species can facilitate hybrid speciation (as in Europe [86]).

Reproductive character displacement is another potential evolutionary outcome of human-caused secondary contact, where mating systems evolve to reduce gene flow between partially incompatible species when in contact. For example, mating to males of the mosquito Aedes albopictus effectively sterilizes females of Ae. aegypti, leading to population declines of the latter where they overlap in range in the Americas, where both species are introduced and invasive [87]. Ae. aegypti have recently evolved lower rates of interspecific mating in sympatry with Ae. Albopictus than in allopatry, a tell-tale sign of reproductive character displacement, reducing gene flow and allowing Ae. aegypti to persist [87].

In addition to increasing contact rates between previously isolated populations, humans are also decreasing contact rates between previously connected populations. Roads, dams, deforestation and other habitat alterations act as anthropogenic vicariance events. Evidence is accumulating that such human-caused isolation events have led to genetic and morphological divergence (e.g. in sticklebacks following the construction of a dam in Iceland [88] in Geoffroy's tamarin following the construction of the Panama canal [89] see also references in [90]). Evidence that such isolation has led to allopatric speciation is, however, lacking, likely reflecting the slower accumulation of reproductive isolating barriers in the absence of strong ecological selection. In the long-term, the fragmentation of species ranges into isolated populations may also increase the rate of speciation, for those species capable of persisting.

(c) Human-altered selection

Finally, speciation rates may be affected by the changing nature and strength of selection in the Anthropocene. With more intensive selection, adaptive mutations are expected to become fixed in different populations at a higher rate, decreasing the expected time until an incompatibility arises between populations according to the ‘snowball’ model of speciation [91].

Potentially even more important than the number of substitutions is the nature of those substitutions. With strong selection induced in human-altered environments [33], genetic changes are more likely to involve large-effect mutations, which our recent research suggests is more likely to lead to speciation. Why? Large-effect mutations are more likely to have stronger deleterious side effects (either due to pleiotropy or hitchhiking) that contribute to reduced fitness of inter-population hybrids. Furthermore, the chance that offspring overshoot a fitness optimum is increased when crossing two lines carrying different large-effect beneficial mutations.

The hypothesis that strong selection is likely to shorten the time to speciation is consistent with our laboratory experiments with yeast. After only days of exposure to the fungicide nystatin, we have observed that independently adapted strains, bearing different large-effect mutations, show reduced ‘hybrid’ fitness (Dobzhansky–Muller incompatibilities) in 33–50% of the crosses [92]. Modelling also confirms this hypothesis. By moving a fitness optimum rapidly versus slowly, we find that large-effect mutations that accumulate in a rapidly changing environment generate stronger reproductive incompatibilities than small-effect mutations that accumulate when the environment changes slowly, even when the populations have reached the same optimum [93].

Similarly, genetic analyses of the Mimulus gutatus populations adapted to mine tailings show that the reproductive incompatibility with surrounding populations is associated with a major-effect mutation at the Tol1 locus [82]. In this case, the strong selection allowed hitchhiking of a linked mutation at the Nec1 locus that is thought to be responsible for the incompatibility.

In summary, there are good reasons to expect more rapid speciation in the Anthropocene [90], particularly in groups evolving into new niches and responding rapidly to selection. In other groups, however, human-caused secondary contact, habitat degradation and environmental homogenization are causing the collapse of what might otherwise have remained or become good species. The net impact of humans on speciation rates, even whether that impact is positive or negative, remains unknown.

6. Conclusion

Humans have altered the course of evolution. The pervasiveness of evolutionary impacts, from genome structure to dispersal rates, on species throughout the globe should make us take pause. Particularly troubling is the elevated extinction rate associated with human activities, which is disproportionately leading to the loss of large-bodied, specialist, narrow-ranged species, as well as species that are otherwise vulnerable to humans.

While the impacts of humans on extinction rates have rightfully received substantial attention, humans are also reshaping the selection pressures within species, favouring organisms that are human-tolerant over those that are human-sensitive, whether sensitive to development, harvesting, anthropogenic climate change, etc. It is worth emphasizing that, in many cases, human-associated selection pressures can be strong, stronger than is typically measured in less impacted systems [36]. There are theoretical reasons to expect that strong selection imposed by humans will lead, as a side consequence, to fitness loss in other attributes of survival and reproduction, with genetic substitutions expected to reduce fitness on average by roughly half the strength of selection imposed by humans on those loci [94]. From morphological changes, such as wing shape and body size, to behavioural changes, such as biting preferences and migration routes, our world is evolving less under the pressures of natural selection and more under the pressures of anthropogenic selection.


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Vol 372, Issue 6537
02 April 2021

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By Mónica R. Carvalho , Carlos Jaramillo , Felipe de la Parra , Dayenari Caballero-Rodríguez , Fabiany Herrera , Scott Wing , Benjamin L. Turner , Carlos D’Apolito , Millerlandy Romero-Báez , Paula Narváez , Camila Martínez , Mauricio Gutierrez , Conrad Labandeira , German Bayona , Milton Rueda , Manuel Paez-Reyes , Dairon Cárdenas , Álvaro Duque , James L. Crowley , Carlos Santos , Daniele Silvestro

Science 02 Apr 2021 : 63-68

Analysis of fossil pollen and leaf assemblages from Colombia tracks the pattern of forest composition into the Paleocene.


Results

Age–Area Relationships Expected under a Stochastic Model of Range Size Evolution

We modelled a process of range evolution and species diversification in which range sizes within lineages evolved according to a random walk through time (see Materials and Methods for details). Within the simulation, we considered two models of speciation rate (either independent or positively correlated with range size) and varied both the rate of change in range size and the asymmetry of range division amongst the daughter lineages during speciation (see Materials and Methods for details). Extinction occurs when the range size of a species walks to or below zero. For each combination of speciation model, rate of range evolution, and range inheritance asymmetry, we ran 500–5,000 replicates of clade diversification and range evolution.

Pooling the results from across replicate clades shows that range size may show strong correlations with species age even under a random model of range size evolution (Figure 1). Range size is positively correlated with evolutionary age across much of the parameter space, and it is evident that high rates of range evolution give rise to stronger positive correlations (Figure 1, unfilled circles), resulting from increased extinction of small-ranged species. In rare circumstances, our stochastic model predicts negative age–area correlations (Figure 1, filled circles). This requires slow rates of range evolution, an increase in the probability of speciation with range size, and high asymmetry in range splitting (Figure 1A). Under this scenario, which resembles a peripatric speciation model [38], small-ranged species are less likely to speciate than large-ranged species but are also unlikely to go extinct. They will therefore tend to occur on the end of longer terminal branches than large-ranged species [27],[39]. In contrast, when speciation rate is independent of range size (Figure 1B), positive age–area correlations are expected even when extinction is negligible. This occurs because range sizes decrease at speciation, and so species with the largest ranges will tend to be those that have not recently undergone speciation.

Variation in Spearman's correlation (ρ) between species' age and geographic range area under different combinations of asymmetry in range size inheritance and rate of change in range size where probability of speciation (ν) increases with range size (A) or is constant (B). Filled circles indicate negative correlations, while unfilled circles indicate positive correlations. Correlations are across all simulated clades for a particular parameter combination. Using a subsample of clades within an example combination (marked with an asterisk) shows that the observed correlation is strongly dependent on clade size (C). Grey boxes highlight the area of parameter space presented in Figure 2.

Although these correlations reveal the overall expected relationship under different scenarios, individual simulations exhibit considerable variation in the correlation between age and area, and pooling smaller sets of simulations shows the extent of this variation (Figure 1C). Therefore, we also calculated the relative frequencies with which individual simulations fall into five broad categories of age–area relationships. To do this, we fitted range size as a quadratic function of species age for each clade in our simulated dataset, using F-tests of the significance of terms to simplify to a linear regression or a null model where appropriate. We aggregated the results of these models into five broad classes: no relationship, increasing relationship, decreasing relationship, intermediate peaks, and intermediate troughs (see Materials and Methods for details) (Figure S1). Our results were qualitatively similar when using more detailed curve classifications (Figures S1 and S4 Table S1).

Observed Age–Area Correlations among Extant Species

We assessed the age–area relationships of individual genera of birds and mammals using the same curve classification procedure as for our simulated clades. Observed clades exhibit a variety of relationships, including positive linear and intermediate troughs, but in only a minority of cases are these age–area relationships significant (9.4% Tables 1, S1, and S2). In accordance with the effects of sample size on statistical power revealed by our simulations (Figure 1C), grouping species into orders (median richness = 29 species) rather than genera (median richness = 12 species) increases the proportion of clades exhibiting significant age–area correlations to 23.5% (Table 1).

Observed versus Simulated Age–Area Correlations in Extant Species

Different combinations of parameter values in the null model give rise to differences in the relationship expected between range size and evolutionary age (Figures 1, 2A, and 2B). One explanation for the variety of age–area correlations observed in the empirical data is therefore that rates of range evolution or the geographic mode of speciation have differed amongst clades. However, when clade sizes are relatively small, as is typical of empirical datasets, we expect to see substantial variation in age–area correlations simply because of chance. To explore this effect, for each point in parameter space, we compared the proportion of observed and simulated clades exhibiting a particular age–area correlation. Because of the strong effect of clade richness on the patterns (Figure 1C), we randomly aggregated our simulated clades until average species richness was similar to that of our empirical dataset. The results for a representative sample of parameter space show that the full spectrum of observed age–area correlations can often arise because of stochastic sampling of the overall null expectation (Figure 2A and 2B). However, the precise frequency of the different age–area curves across avian and mammalian clades cannot generally be explained by any single combination of parameters (Figure 2A and 2B). Overall the results suggest that while substantial variation in age–area correlations observed across clades may be due to chance, differences in the rates of range evolution or modes of geographic speciation across clades may also be required.

The grey bars show the 95% confidence limits of the expected relative proportion of different age–area relationship classes under different combinations of asymmetry and range size inheritance for extant vertebrates (A and B) and extinct molluscs (C and D). The probability of speciation (ν) increases with range size (A and C) or is constant (B and D). Observed proportions of each class are shown as black bars for vertebrate orders (Table 1) and mollusk species (Table S3) shorter bars in (A) and (B) show the proportions for bird (left) and mammal (right) orders separately. The nine panels in each block correspond to the highlighted areas of Figure 1.

Range Size Trajectories of Extinct Species in the Fossil Record and the Stochastic Model

To investigate whether the stochastic model can account for the patterns observed in the fossil record, we extracted the extinct lineages from our simulations and assigned each one of these to a range size trajectory. To ensure that the definition of species age in our simulations was consistent with the empirical data, we measured absolute species ages under a model of ancestral persistence: upon each speciation event the lineage with the larger range size retained the ancestral species name, with the smaller ranged lineage designated as a new species. Species ages thus represent the time between the first and last occurrence of a species and are not affected by the speciation or extinction of other lineages [40].

The empirical dataset consists of the occupancy trajectories of extinct marine mollusks provided by Foote et al. [7]. Because many (44%) of the species occurred in only three statigraphic stages we did not attempt to fit curves to these and instead assigned each species to one of three possible range trajectories, depending on whether its peak mean range size was reached in the first, second, or third tercile of its life (see Materials and Methods for details). If range size is independent of evolutionary age, then a similar proportion of species should reach their maximum extent across each of the three sampling intervals. We used exactly the same procedure for assigning range size trajectories in our simulated dataset.

We found that approximately 57% of mollusk species reached their peak range size in the middle of their lives, with the number of peaks in the first and final third relatively evenly split (Figure 2C and 2D Table S3). Our analysis therefore supports the pattern of “rise and fall” previously reported for this group (multinomial model: p<0.017). However, our stochastic model shows that when geographic ranges have evolved randomly through time, range size is not expected to be independent of species age (Figure 2C and 2D). Instead, most species are expected to reach their maximum geographic extent in either the first or second interval of their lives, and typically have smaller ranges at the end of their durations (Figure 2C and 2D). This occurs because extinct species must have undergone a net decline in range size through time, and, when ranges evolve according to a random walk, extinction is likely to be preceded by rarity unless rates of range evolution are extremely high.

Whether species undergo a continuous decline or exhibit an intermediate peak depends on the probability of extinction amongst newly formed species (Figure 2C and 2D). When young species have a low probability of extinction, either because they inherit a large range or because ranges are relatively stable, then the predominant pattern is for range sizes to simply decline through time (Figure 2C and 2D). In contrast, when species inherit a small geographic range or when rates of range evolution are high, then only those species that initially expand their distributions are likely to persist for a sufficient length of time to be included in the analysis (i.e., more than two time steps see Materials and Methods for details) (Figure 2C and 2D). Under these conditions the relative frequency of the different range size trajectories observed across marine mollusks is consistent with that expected under a stochastic model (Figure 2C and 2D).


Background

Today, humans are the dominant animal species on Earth, and we have both a direct (dramatically changing land surfaces by settlements) [1, 2] and indirect influence on the Earth’s climate [3,4,5], consequently changing the physiology, behaviour, and evolution trajectories of all other organisms [6,7,8,9]. The impact of climate warming is so strong that it influences almost everything from microorganisms to plant and animal populations. Climate change accelerates plant extinction by changing their phenology, e.g., mismatching the flowering period of plants with pollinating time of insects [10, 11] and narrowing the range of physiological adaptation, thus reducing plant resistance to extreme weather events [12, 13]. These effects are particularly substantial in hotspot areas of plant diversity in the tropics and subtropics [14,15,16,17,18,19]. On the other hand, climate warming has led to increased global vegetation activity, providing more resources and better hydrothermal conditions which are necessary for the evolution of new species [8, 20,21,22,23,24]. Recently, it has been observed that the plant diversity at a mountaintop increased significantly under the influence of climate warming [25], and studies have also showed that plant diversity continued to increase at high latitudes [26], leading to the conclusion that the Anthropocene is and will continue to be the golden age for the evolution of new species. The accelerated plant speciation in natural and unnatural ecosystems during this or the following centuries [23, 27,28,29,30] means that we will witness a world of diverse plants thriving in new environmental conditions. The two abovementioned viewpoints propose contrasting scenarios, i.e., the first indicates that plant speciation is accelerating in the Anthropocene, whereas the second indicates that plant extinction is simultaneously accelerating. The question that is important to address is if plant diversity will increase or decrease in this and following centuries [9].

Considering the development and utilization of plant resources, during the last 10,000 years, we have gradually acquired immense knowledge of plant species. Since the end of the Last Glacial Maximum, the Earth’s climate has warmed. The establishment of human settlements led to the development of agriculture and consequently, the development of modern civilization. Agriculture is a symbol of human civilization [31] and it is inseparable from plant domestication. Today, steamed bread made from hexaploid wheat, triploid banana, and seedless watermelons are consumed daily throughout the world, oils are extracted from tetraploid peanuts and clothing is made from tetraploid cotton. Domesticated plants, which some of them are polyploids, have higher leaf nitrogen content, higher growth rate and bigger seeds than those of their diploid ancestors, as polyploids with larger genome sizes are more resistant to adverse effects of genetic mutations [32, 33]. Today, the cultivation and management of polyploid crops support a population of 7.7 billion. Polyploid species generally evolve as a consequence of doubling of the chromosomes of the ancestral diploid. In recent times, the technology of inducing neopolyploidy by physical and chemical agents has been developed and is used in research. However, the technology used today for developing new polyploids is essentially the same as polyploidization in nature, except that the breeding cycle is greatly shortened using novel methods [34]. Compared with the human technology for developing neopolyploids, in nature, new species often evolve because of climate or environmental changes [29, 34,35,36].

The dominant plant speciation type in nature

Even though humans have been breeding new plant species for the past few thousand years, more focus has been placed on plant extinction than on plant speciation (Fig. 1) [37]. With the acceleration of climate warming, plant speciation caused by warming climate may become a more common phenomenon in this and following centuries [27]. Human civilization supports itself by intensive exploitation and utilisation of fossil energy accumulated approximately 300 million years ago (Mya). The CO2 emissions from a large number of fossil combustions are the main factor contributing to warmer climate and associated issues, such as ocean acidification and species extinction. Species extinction and conservation are important matters of public concern (Fig. S1). Comparing the extinction risk of species, the formation of new plant species is thought to be currently constrained in the academic world [27], this is partly because people (non-scientists) become aware of species extinction reports (Fig. 1 Fig. S1). However, plant speciation through polyploidization may be quite common, and autopolyploidy, which is caused by the polyploidization of two conspecific individuals, is presumed to be the dominate [27, 28, 34] (Fig. 2). On the other hand, allopolyploids are the result of interspecific hybridization process and chromosome duplication. Speciation as a consequence of chromosomal rearrangements, homoploid hybrid speciation, and lineage splitting are not common because of their long evolutionary time and low occurrences, e.g., it takes several thousand years for a new plant species to evolve through lineage splitting [39].

Differences of public and scientific attention to plant speciation and extinction. The public is more concerned with plant extinction (a), whereas scientists have a greater interest in plant speciation (b). We used Google Ngram’s millions of English-language books [37] to quantify the public attention on “plant speciation” and “plant extinction” during 1980–2008. The cumulative word frequency is 6.4 × 10 − 8 and 8.0 × 10 − 8 for plant speciation and extinction, respectively. We searched the core database of Web of Science for the publication of “plant speciation” and “plant extinction” during 1980–2018 to illustrate the academic concerns. The cumulative published papers are 6946 and 6651 on “plant speciation” and “plant extinction”, respectively. The searched research field was plant science, and the selected 10 journals of evolution and ecology: Annual Review of Ecology Evolution and Systematics, Biology Letters, BMC Evolutionary Biology, Evolution, Evolutionary Applications, Evolutionary Biology, Evolutionary Ecology, Proceedings of the Royal Society B-Biological Sciences, Systematic Botany, and Trends in Ecology & Evolution

A simplified conceptual model depicting the types of plant speciation and the drivers of plant extinction in the Anthropocene. Three identified plant speciation accelerators, i.e., cities, polar regions, and botanical gardens are illustrated to show how climate warming might change plant evolution in the future. The contribution to plant speciation displayed from the top to bottom are: autopolyploid speciation, allopolyploid speciation, and chromosomal rearrangements. The main drivers of plant extinction displayed from right to left are: habitat loss, deforestation, land use change, climate change, and pollution. The solid lines denote the biological and ecological processes of plant speciation and extinction, in which the green ones denote the corresponding speciation types, and the red ones denote the five drivers of plant extinction. The thickness of the arrow denotes the relative strength of the contributions. It should be noted that climate change accelerates plant speciation while drives plant extinction either, and human population increase as the primary driver of plant extinction. Both new plant species and their progenitors of plant species may face same extinction risk in the Anthropocene, but the new plant species are more likely to survive due to their stronger natural adaptability to climate change [38]

Speciation accelerated by the greenhouse effect

Understanding that autopolyploid speciation is the most dominant speciation type in the Anthropocene requires a view from the perspective of plant evolution. The Earth has experienced extensive climatic fluctuations since its birth. The first plants are nearly omnipresent on Earth and they often survive climatic fluctuations via whole genome duplication, i.e., polyploidization [35]. For example, many species of ferns, gymnosperms, and angiosperms have undergone multiple whole genome duplications during their long evolution [40]. The main biological determinant of plant survival is their genome multiplication. For example, during the warm period of the Palaeocene–Eocene Thermal Maximum (PETM) 55.8 Mya, when the Earth experienced temperatures 5–8 °C higher than those today, the multiplication of the genomes of many angiosperm species occurred [38, 41, 42]. Multiplications provided angiosperms the advantage in surviving sudden climate changes by giving them a competitive growth advantage, and they were eventually established as the most successful plant lineage [36, 40, 43,44,45,46,47]. While climate warming could disturb germline development and lead to reduced fitness in some plant species [48], plants could also evolve to adapt because the production of unreduced gametes that facilitates autopolyploidization is positively correlated with nutrient (e.g., nitrogen deposition and crops fertilization), humidity (e.g., floods and reduced surface runoff due to elevated CO2), temperature variation (e.g., heat waves) and high levels of herbivory (i.e., bark beetle and caterpillars outbreaks) that likely to be encountered under future climate change scenarios [27, 34]. Considering that the climate at the end of this century could resemble that during PETM [49], and if greenhouse gas emissions are not significantly reduced, it is reasonable to infer that plants will experience polyploidy of a similar magnitude.

Mechanisms underlying plant speciation

Review the past to understand the present. According to the Representative Concentration Pathway 8.5 (RCP 8.5) emission scenario, climate warming today might promote polyploidy to a similar extent to that during PETM. The question is, what are the biological or ecological mechanisms underlying the increase in polyploidization? There are two possible reasons for this increase [34, 48]: (i) the first is high temperature induction of chromosome doubling. In a newly fertilized immature embryo or germ cell, active division occurs, meaning it is easy to induce polyploidy by sudden temperature increases (but not as high as to cause cell death). Autotetraploid corn was developed using this method prior to the discovery and extensive use of colchicine (ii) Climate warming leads to the extension of the growing season. This increases the chances of contacts among plants, and thus sympatric speciation emerges as the dominant speciation type [50]. Significant results of climate warming are the advance of budding and the delay in leaf shedding, both of which prolong the growing season [51]. These scenarios favour the breakage of prezygotic barriers. In the foreseeable future, climate warming will be the dominant climatic feature of this and the following centuries [52], thereby ensuring the occurrence of autopolyploid speciation [35].

Accelerators of plant speciation

Plant resources determine the sustainable development of human society, and thus, nearly all countries have made great efforts to establish protected areas to maintain their plant diversity [53, 54]. A large number of protected areas worldwide have significantly reduced habitat loss [55,56,57], and large unexplored wilderness areas have reduced the risk of plant extinction by at least 50% [58]. Compared to larger and more effective protected areas (

23%) [59], urban development areas account for only

1% of land surface area [60], but they have extremely significant effects on plant phenology, physiology, ecology, and heredity [61,62,63]. In addition, the genetics of the plant species in botanical gardens are also significantly different from their wild congeners [64]. In the Anthropocene, the three accelerators that have a significant effect on driving plant species evolution are cities, the polar amplification of climate change, and botanical gardens which are believed to play both the role of “cradle” and “museum”.

Accelerator I: cities

One of the most prominent features of the Anthropocene are man-made clusters of large buildings and cities. As a “natural laboratory”, the city is an ideal environment for monitoring the rapid evolution of plants [65]. Cities are inhabited by more than 50% of the world’s population and consume

80% of global energy [60]. As a consequence of the pronounced “heat island effect”, it has been predicted that urban development will become an accelerator of plant speciation. The temperatures of most cities are

1 °C higher than those of the surrounding non-urban areas, and the temperatures in humid regions or densely populated cities can be even 1.5 °C higher than those of the surrounding non-urban areas [66]. Therefore, the climate of cities today is comparable to the predicted climate at the end of the century (equivalent to significant carbon mitigation in the RCP 2.6 scenario). As most urban plant species are native species with strong adaptability [67, 68], and most importantly, because these native urban plants are planted and grown only in extremely limited space, these plants are more likely to undergo autopolyploid speciation than any other speciation type [65].

Accelerator II: polar regions

As a consequence of polar amplification [69], the Arctic may be the fastest warming region on Earth compared to the global average (0.60 vs. 0.17 °C/decade) [70]. Melting ice further reduces solar radiation reflections, which further accelerates the melting of glaciers, eventually leading to an ice-free summer predicted for the eve of 2030 [71,72,73]. The warm Arctic waters are favourable for phytoplankton [74], and the increase in phytoplankton significantly increases the primary producers’ provision for marine animals, which in turn promotes the prosperity of biodiversity [75]. Polar regions (including Antarctica and the Qinghai-Tibet Plateau) have always been the centre of plant divergence [76, 77], and they may play more of a “cradle” role in the context of climate warming. It has recently been found that the number of plant species has significantly increased in the Arctic [26], which might have been a consequence of diffusion or migration [78] rather than speciation, suggesting a “museum” role of the polar regions. With the further warming of the global climate, especially in the Antarctic [79, 80] and the “Third Pole”, i.e., Qinghai-Tibet Plateau [81] that have similar temperature increase amplitudes to the Artic, new species may evolve from alien and native species through hybridization or autopolyploid speciation in these polar regions.

Accelerator III: botanical gardens

Early plant gatherers collected exotic plants and planted them in small areas today, these areas would be called botanical gardens. Botanical gardens are spread worldwide because of their practical functions, such as cultural and recreational function as well as medicinal plant preservation [82]. When plant gatherer Ernest Henry Wilson brought thousands of plant species from China and Asia to Kew Botanic Garden, he could not have known that his actions would inadvertently lead to the evolution of a new species, Primula kewensis [23], as well as many other new plant species (cf. Chris D. Thomas’s papers). There is a possibility that some epiphytic orchids in the botanical garden are currently undergoing rapid speciation [64]. The attraction of people to ornamental flowers has led to the development of new species of orchids and primroses [83, 84], indicating that botanical gardens can be used as cradles of speciation. The main reason why botanical gardens are a major factor in the evolution of new species is that a large number of plants gathered in a small area increases the probability of interspecific pollen transmission via pollinating insects. Therefore, in addition to autopolyploid speciation, allopolyploidy and hybrid speciation are also important in plant evolution in these artificial gardens [23, 24, 29, 85,86,87,88]. Botanical gardens preserve

40% of endangered plants on the Earth, and thus they have an extremely important conservation function [89]. One of the most obvious features is that the plants found in botanical gardens may have come from any corner of the world [90]. Therefore, the contribution of allopatric and that of sympatric speciation to the evolution of new species may be equally important.

Bigger extinction

The alarming risk of extinction

Polyploidy promotes genetic diversity, which is why it is a common plant strategy for surviving climate change [27]. The accelerated speciation under climate warming conditions enhances their adaptation and resilience to climate change, which is necessary to maintain plant biodiversity and crucial for survival. For example, fossil evidence suggests that plants were resilient to mass extinction [91], and had fewer extinctions compared to marine fauna. Under the climate warming scenario, the resulting accelerated plant speciation could be 50–300 times faster than background speciation, and this rate is far lower than the current rate of plant extinction. In contrast, the rate of plant extinction in the Anthropocene is 1000–10,000 times higher compared to that of the background extinction [27, 92]. Therefore, as a consequence of mankind’s inconsiderate exploitation of the Earth’s resources, as well as land-use changes, habitat loss and international trade [9, 93], the risk of plant extinction is much higher than the possibility of plant speciation (Fig. 2). For example, Marques et al. (2019) estimated that 33% of Central and Southern America and 26% of Africa’s biodiversity were influenced by consumption in other world regions [93].

The worsening tropics

Although the risk of plant extinction in Europe (non-tropical areas) is not high, and regional plant diversity may be increasing, the abundance of plant species in the tropical regions with highest species richness (i.e., Congo, Amazon, and Southeast Asia) [94] is decreasing and that’s why the risk of global overall plant extinction still appears to be very high [15, 16, 95]. For example, 58% of tree species in Amazonia are predicted to go extinct in the following 30 years under the pressures of deforestation and climate change [94].

Trophic cascading

The indirect effects of anthropogenic activities may be more devastating to plants than we perceive. The annual decline in insect biomass is estimated to be 2.5% worldwide [96]. As insects are the basis of terrestrial and aquatic food chains, the increase in prezygotic barriers would be devastating for plant diversity [87]. For example, in some very small populations of endangered plants, the decrease in the number of pollinating insects can increase the pollen limit, thus increasing the risk of extinction [97, 98]. The decrease in the number of pollinating insects negatively affects not only endangered plants, but almost all plants that are pollinated by insects, especially certain crops crucial for agriculture [99, 100]. In recent years, large-scale use of chemicals such as neonicotinoid pesticides has caused irreversible damage to bee populations [101,102,103]. Even worse, the dramatic decline in bird populations is similar to the dramatic decline in insect populations. For instance, a recent study showed that North American avifauna has decreased by 3 billion over the past half century, which is equivalent to

30% of the total number of birds in the 1970s [104]. Today, the sharp decline in bird populations as a consequence of habitat loss because of agricultural activities, urbanization, and toxic pesticide use in both breeding and wintering areas is a global problem [105, 106]. Pollinating insects and birds are directly related to plant life histories (e.g., reproduction and seed dispersal), which is why their continuous and significant decrease in numbers will have a significant negative impact on plant diversity [99, 107,108,109].

Humans determine plants extinction directly and globally

In the next ten years, the global population is predicted to reach 8.5 billion [110] and surge to 9.7 billion and 11 billion in the middle and the end of this century, respectively [111]. Such a large population will have significant impacts on the Earth’s resources and natural ecosystems [112, 113]. In order to feed such a large population, 100–110% increase in global crop supply must be achieved by the middle of this century, which means that without the implementation of high-efficient agriculture, arable land area will have to increase by approximately 1 billion ha [114]. In order to achieve this, deforestation will be unavoidable [115, 116], which will cause a large number of forests to be converted into agricultural land and settlements [31, 117], and these land-use conversions will lead directly to plant habitat loss, which is the direct reason of plant extinction [18] (Fig. 2). Therefore, deforestation and land use change can be considered as the main and direct causes of plant extinction, whereas climate change and pollution are indirect (or possibly partly direct) causes of plant extinction [118]. It has been predicted that heavy metal and synthetic chemical pollution will change pollen morphology and physiological functions of plants, leading to the extinction of terrestrial plant species [119, 120], and excessive use of nitrogen and phosphorus fertilizers in agriculture leads to eutrophication and extinction of both terrestrial and aquatic plant species [121, 122].

In addition, fire [123] or outbreaks of pests [124] and invasive plants [125], which can be indirect effects of climate change, will also significantly increase the risk of plant extinction. The driving forces of plant extinction are not mutually exclusive [14, 126]. For example, land use change is the result of deforestation, which can further enhance the effects of climate change because the deforested areas are more negatively influenced by unstable climate extremes than forested areas. Deforestation and the corresponding habitat loss are direct causes of plant extinction [126], but by the middle of this century, their negative impacts could be surpassed by the negative impacts of climate change [94]. But here, climate change, mainly means a warming climate, is supposed to have a more significant effect on plant speciation [24, 127]. However, the positive effect of climate change on plant speciation was greatly reduced and reversed by land use change, deforestation, and habitat loss. Therefore, in the Anthropocene, the rate of plant speciation is much lower than the rate of plant extinction [128]. In all, the primary cause of plant extinction is the uncontrolled exploitation of the Earth’s resources in order to maintain human population growth and quality of life [93, 129, 130].


A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary

Figure S2. Power to detect sequential mass-extinction events.

Figure S3. Frequency of detecting spurious mass-extinction events when tree-wide radiations are modeled as bursts in the speciation rate.

Figure S4. Frequency of detecting spurious mass-extinction events when tree-wide radiations are modeled as bursts in the net-diversification rate.

Figure S5. Frequency of detecting spurious mass-extinction events under the speciation-rate slowdown model.

Figure S6. Frequency of detecting spurious mass-extinction events under the lineage-specific diversification-rate model.

Figure S7. Ability to estimate the magnitude of mass-extinction events under the CoMET model.

Figures S8 and S9. False-discovery rates.

Figures S10 and S11. Power as a function of time.

Figures S12 and S13. Bias in estimates of mass-extinction time.

Figure S14. Empirical hyperpior analysis of the conifers.

Figure S15. Bayes factors for conifer analyses under various priors.

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3.19: Speciation and extinction - Biology

Geographic isolation
In the fruit fly example, some fruit fly larvae were washed up on an island, and speciation started because populations were prevented from interbreeding by geographic isolation. Scientists think that geographic isolation is a common way for the process of speciation to begin: rivers change course, mountains rise, continents drift, organisms migrate, and what was once a continuous population is divided into two or more smaller populations.

It doesn't even need to be a physical barrier like a river that separates two or more groups of organisms — it might just be unfavorable habitat between the two populations that keeps them from mating with one another.

Reduction of gene flow
However, speciation might also happen in a population with no specific extrinsic barrier to gene flow. Imagine a situation in which a population extends over a broad geographic range, and mating throughout the population is not random. Individuals in the far west would have zero chance of mating with individuals in the far eastern end of the range. So we have reduced gene flow, but not total isolation. This may or may not be sufficient to cause speciation. Speciation would probably also require different selective pressures at opposite ends of the range, which would alter gene frequencies in groups at different ends of the range so much that they would not be able to mate if they were reunited.

Even in the absence of a geographic barrier, reduced gene flow across a species' range can encourage speciation.


Biology: the essentials 2nd

How has the meaning of the term species changed since the time of Linnaeus?

Problem 2

What type of reproductive barrier applies to each of these scenarios?
mathrm

1800 s.
Insects called hawthorn flies, which feed and mate on hawthorn plants, quickly discovered the new fruits. Some flies preferred the taste of apples to their native host plants. Because these flies mate where they eat, this difference in food preference quickly led to a reproductive barrier.
b. Water buffalo and cattle can mate with each other, but the embryos die early in development.
c. Scientists try to mate two species of dragonfly that inhabit the same pond at the same time of day. However, females never allow males of the other species to mate with them.
d. One species of reed warbler is active in the upper parts of the tree canopy while another species of reed warbler is active in the lower canopy. Both species are active during the day.
Scientists mate two parrots from different populations to see if speciation has occurred. The parrots mate over and over again, but the male's sperm never fertilizes the female's egg.


Watch the video: Lecture 11 Speciation and Extinction (May 2022).


Comments:

  1. Mikajar

    It - is improbable!

  2. Salhdene

    It can be discussed endlessly.

  3. Zulkilabar

    Excuse, that I interrupt you, but it is necessary for me little bit more information.

  4. Magul

    In my opinion a very interesting topic. I suggest you discuss this here or in PM.



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