High speciation rate at temperate latitudes explains unusual diversity gradients in a clade of ectomycorrhizal fungi

Understanding the patterns of biodiversity through time and space is a challenging task. However, phylogeny‐based macroevolutionary models allow us to account and measure many of the processes responsible for diversity buildup, namely speciation and extinction. The general latitudinal diversity gradient (LDG) is a well‐recognized pattern describing a decline in species richness from the equator polewards. Recent macroecological studies in ectomycorrhizal (EM) fungi have shown that their LDG is shifted, peaking at temperate rather than tropical latitudes. Here we investigate this phenomenon from a macroevolutionary perspective, focusing on a well‐sampled group of edible EM mushrooms from the genus Amanita—the Caesar's mushrooms, which follow similar diversity patterns. Our approach consisted in applying a suite of models including (1) nontrait‐dependent time‐varying diversification (Bayesian analysis of macroevolutionary mixtures [BAMM]), (2) continuous trait‐dependent diversification (quantitative‐state speciation and extinction [QuaSSE]), and (3) diversity‐dependent diversification. In short, results give strong support for high speciation rates at temperate latitudes (BAMM and QuaSSE). We also find some evidence for different diversity‐dependence thresholds in “temperate” and “tropical” subclades, and little differences in diversity due to extinction. We conclude that our analyses on the Caesar's mushrooms give further evidence of a temperate‐peaking LDG in EM fungi, highlighting the importance and the implications of macroevolutionary processes in explaining diversity gradients in microorganisms.     

Digest: The contribution of historical climate events in shaping the modern latitudinal diversity gradient of ancient reptiles

It is recognized that biodiversity changes across the planet latitudinally; however, the timing of and reasons for diversity loss at higher latitudes are not well understood. Meseguer and Condamine investigate phylogenies and fossil evidence of reptilian species and determine that global warming and cooling events allowed asymmetric extinction and dispersion across latitudes, suggesting a hypothesis where climate profoundly shapes the latitudinal diversity gradient in certain taxa.     

Revisiting Jablonski (1993): cladogenesis and range expansion explain latitudinal variation in taxonomic richness

The increase in diversity towards the equator arises from latitudinal variation in rates of cladogenesis, extinction, immigration and/or emigration of taxa. We tested the relative contribution of all four processes to the latitudinal gradient in 26 marine invertebrate orders with extensive fossil records, examined previously by David Jablonski. Coupling Jablonski's estimates of latitudinal variation in cladogenesis with new data on patterns of extinction and current distributions, we show that the present-day gradient in diversity is caused by higher rates of cladogenesis and subsequent range expansion (immigration) at lower latitudes. In contrast, extinction and emigration were not important in the creation of the latitudinal gradient in ordinal richness. This work represents one of the first simultaneous tests of the role of all four processes in the creation of the latitudinal gradient in taxonomic richness, and suggests that low tropical extinction rates are not essential to the creation of latitudinal diversity gradients.     

Primate diversification inferred from phylogenies and fossils

Biodiversity arises from the balance between speciation and extinction. Fossils record the origins and disappearance of organisms, and the branching patterns of molecular phylogenies allow estimation of speciation and extinction rates, but the patterns of diversification are frequently incongruent between these two data sources. I tested two hypotheses about the diversification of primates based on ～600 fossil species and 90% complete phylogenies of living species: (1) diversification rates increased through time; (2) a significant extinction event occurred in the Oligocene. Consistent with the first hypothesis, analyses of phylogenies supported increasing speciation rates and negligible extinction rates. In contrast, fossils showed that while speciation rates increased, speciation and extinction rates tended to be nearly equal, resulting in zero net diversification. Partially supporting the second hypothesis, the fossil data recorded a clear pattern of diversity decline in the Oligocene, although diversification rates were near zero. The phylogeny supported increased extinction ～34 Ma, but also elevated extinction ～10 Ma, coinciding with diversity declines in some fossil clades. The results demonstrated that estimates of speciation and extinction ignoring fossils are insufficient to infer diversification and information on extinct lineages should be incorporated into phylogenetic analyses.     

Origins of marine patterns of biodiversity: some correlates and applications

Abstract: Marine shelf diversity patterns correlate with macroecological features of basic importance that may play causal roles in macroevolution. We have investigated the global diversity pattern of living Bivalvia, which is dominated by the latitudinal diversity gradient (LDG), maintained by high tropical origination rates. Generic‐level lineages expand poleward, chiefly through speciation, so that species richness within provinces and globally is positively correlated with generic geographical ranges. A gradient in diversity accommodation progressively lowers both immigration and speciation rates in higher latitudes. The LDG correlates with seasonality of trophic resources but not with area; tropical provinces are not diverse because they are large but because they are tropical. A similar dynamic evidently underlays Jurassic and Carboniferous LDGs. Larval developmental modes correlate with the LDG and thus with resource seasonality, with tropical dominance of planktotrophs offset by increasing nonplanktotrophy to poleward. The acquisition of planktotrophy in several early Palaeozoic clades indicates a change in macroecological relationships during Cambrian and Ordovician radiations.     

The tropics: cradle,museum or casino? A dynamic null model for latitudinal gradients of species diversity

Several ecological and evolutionary hypotheses have been proposed to explain the latitudinal diversity gradient (LDG), but a general model for this conspicuous pattern remains elusive. Mid-domain effect (MDE) models generate gradients of species diversity by randomly placing the geographic ranges of species in one- or two-dimensional spaces, thus excluding both evolutionary processes and the effect of contemporary climate. Traditional MDE models are statistical and static because they determine the size of ranges either randomly or based on empirical frequency distributions. Here we present a simple dynamic null model for the LDG that simulates stochastic processes of range shifts, extinction and speciation. The model predicts higher species diversity and higher extinction and speciation rates in the tropics, and a strong influence of range movements in shaping the LDG. These null expectations should be taken into consideration in studies aimed at understanding the many factors that generate latitudinal diversity gradients.     

Latitude and rates of diversification in birds and butterflies

Central to many explanations of latitudinal diversity gradients is the idea that rates of species diversification increase towards the equator. However, there have been few explicit tests of whether or not this pattern exists. Using sister-group analyses to compare 48 clades of passerine birds and swallowtail butterflies from different latitudes, I found evidence that relative rates of diversification per unit time are indeed higher towards the equator. This pattern is explicable in terms of abiotic factors which vary continuously with latitude, and may be further enhanced by diversity-dependent speciation and extinction processes.     

Explaining global variation in the latitudinal diversity gradient: Meta‐analysis confirms known patterns and uncovers new ones

Aim

The pattern of increasing biological diversity from high latitudes to the equator [latitudinal diversity gradient (LDG)] has been recognized for > 200 years. Empirical studies have documented this pattern across many different organisms and locations. Our goal was to quantify the evidence for the global LDG and the associated spatial, taxonomic and environmental factors. We performed a meta‐analysis on a large number of individual LDGs that have been published in the 14 years since Hillebrand's ground‐breaking meta‐analysis of the LDG, using meta‐analysis and meta‐regression approaches largely new to the fields of ecology and biogeography.

Location

Global.

Time period

January 2003–September 2015.

Major taxa studied

Bacteria, protists, plants, fungi and animals.

Methods

We synthesized the outcomes of 389 individual cases of LDGs from 199 papers published since 2003, using hierarchical mixed‐effects meta‐analysis and multiple meta‐regression. Additionally, we re‐analysed Hillebrand's original dataset using modern methods.

Results

We confirmed the generality of the LDG, but found the pattern to be weaker than was found in Hillebrand's study. We identified previously unreported variation in LDG strength and slope across longitude, with evidence that the LDG is strongest in the Western Hemisphere. Locational characteristics, such as habitat and latitude range, contributed significantly to LDG strength, whereas organismal characteristics, including taxonomic group and trophic level, did not. Modern meta‐analytical models that incorporate hierarchical structure led to more conservative and sometimes contrasting effect size estimates relative to Hillebrand's initial analysis, whereas meta‐regression revealed underlying patterns in Hillebrand's dataset that were not apparent with a traditional analysis.

Main conclusions

We present evidence of global latitudinal, longitudinal and habitat‐based patterns in the LDG, which are apparent across both marine and terrestrial realms and over a broad taxonomic range of organisms, from bacteria to plants and vertebrates.     

Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record

The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there are often limits to diversity. Here, we present a general approach to evaluate the likelihood of a phylogeny under a model that accommodates diversity-dependence and extinction. We find, by likelihood maximization, that extinction is estimated most precisely if the rate of increase in the number of lineages in the phylogeny saturates towards the present or first decreases and then increases. We demonstrate the utility and limits of our approach by applying it to the phylogenies for two cases where a fossil record exists (Cetacea and Cenozoic macroperforate planktonic foraminifera) and to three radiations lacking fossil evidence (Dendroica, Plethodon and Heliconius). We propose that the diversity-dependence model with extinction be used as the standard model for macro-evolutionary dynamics because of its biological realism and flexibility.     

Latitudinal gradients of parasite richness: a review and new insights from helminths of cricetid rodents

The latitudinal diversity gradient (LDG), or the trend of higher species richness at lower latitudes, has been well documented in multiple groups of free‐living organisms. Investigations of the LDG in parasitic organisms are comparatively scarce. Here, I investigated latitudinal patterns of parasite diversity by reviewing published studies and by conducting a novel investigation of the LDG of helminths (parasitic nematodes, trematodes and cestodes) of cricetid rodents (Rodentia: Cricetidae). Using host–parasite records from 175 parasite communities and 60 host species, I tested for the presence and direction of a latitudinal pattern of helminth richness. Additionally, I examined four abiotic factors (mean annual temperature, annual precipitation, annual temperature range and annual precipitation range) and two biotic variables (host body mass and host diet) as potential correlates of parasite richness. The analyses were performed with and without phylogenetic comparative methods, as necessary. In this system, helminths followed the traditional LDG, with increasing species richness with decreasing latitude. Nematode richness appeared to drive this pattern, as cestodes and trematodes exhibited a reverse LDG and no latitudinal pattern, respectively. Overall helminth richness and nematode richness were higher in areas with higher mean annual temperatures, annual precipitation and annual precipitation ranges and lower annual temperature ranges, characteristics that often typify lower latitudes. Cestode richness was higher in areas of lower mean annual temperatures, annual precipitation and annual precipitation ranges and higher annual temperature ranges, while trematode richness showed no relationship with climate variables when phylogenetic comparative methods were used. Host diet was significantly correlated with cestode and trematode species richness, while host body mass was significantly correlated with nematode species richness. Results of this study support a complex association between parasite richness and latitude, and indicate that researchers should carefully consider other factors when trying to understand diversity gradients in parasitic organisms.     

THE ROLE OF CLIMATIC TOLERANCES AND SEED TRAITS IN REDUCED EXTINCTION RATES OF TEMPERATE POLYGONACEAE

The latitudinal diversity gradient (LDG) is one of the most striking and consistent biodiversity patterns across taxonomic groups. We investigate the species richness gradient in the buckwheat family, Polygonaceae, which exhibits a reverse LDG and is, thus, decoupled from dominant gradients of energy and environmental stability that increase toward the tropics and confound mechanistic interpretations. We test competing age and evolutionary diversification hypotheses, which may explain the diversification of this plant family over the past 70 million years. Our analyses show that the age hypothesis, which posits that clade richness is positively correlated with the ecological and evolutionary time since clade origin, fails to explain the richness gradient observed in Polygonaceae. However, an evolutionary diversification hypothesis is highly supported, with diversification rates being 3.5 times higher in temperate clades compared to tropical clades. We demonstrate that differences in rates of speciation, migration, and molecular evolution insufficiently explain the observed patterns of differential diversification rates. We suggest that reduced extinction rates in temperate clades may be associated with adaptive responses to selection, through which seed morphology and climatic tolerances potentially act to minimize risk in temporally variable environments. Further study is needed to understand causal pathways among these traits and factors correlated with latitude.     

Genetic diversity within vertebrate species is greater at lower latitudes

The latitudinal gradient of species diversity is one of the oldest recognized patterns in biology. While the cause of the pattern remains debated, the global signal of greater diversity toward the tropics is widely established. Whether the pattern holds for genetic diversity within species, however, has received much less attention. We examine latitudinal variation of intraspecific genetic diversity by contrasting nucleotide distance within low- and high-latitude animal groups. Using mitochondrial DNA markers across 72 vertebrate species that together span six continents, two oceans, and 129 degrees of latitude, we found significantly greater genetic diversity at low latitudes within mammalian species, and trends consistent with this pattern in reptiles, amphibians, fish, and birds. The signal held even after removing species whose current geographic ranges include areas recently covered by glaciers during the late Pleistocene and which presumably have experienced colonization bottlenecks in high latitudes. Higher genetic diversity within species was found at low latitudes also for genera that do not possess higher species richness toward the tropics. Moreover, examination of a subset of species with sufficient sampling across a broad geographic range revealed that genetic variation demonstrates a typical gradient, with mid-latitude populations intermediate in genetic diversity between high and low latitude ones. These results broaden the pattern of the global latitudinal diversity gradient, to now include variation within species. These results are also concordant with other studies indicating that low latitude populations and species are on different evolutionary trajectories than high latitude ones, and we speculate that higher rates of evolution toward the equator are driving the pattern for genetic diversity within species.     

Extinction can be estimated from moderately sized molecular phylogenies

Hundreds of studies have been dedicated to estimating speciation and extinction from phylogenies of extant species. Although it has long been known that estimates of extinction rates using trees of extant organisms are often uncertain, an influential paper by Rabosky (2010) suggested that when birth rates vary continuously across the tree, estimates of the extinction fraction (i.e., extinction rate/speciation rate) will appear strongly bimodal, with a peak suggesting no extinction and a peak implying speciation and extinction rates are approaching equality. On the basis of these results, and the realistic nature of this form of rate variation, it is now generally assumed by many practitioners that extinction cannot be understood from molecular phylogenies alone. Here, we reevaluated and extended the analyses of Rabosky (2010) and come to the opposite conclusion—namely, that it is possible to estimate extinction from molecular phylogenies, even with model violations due to heritable variation in diversification rate. Note that while it may be tempting to interpret our study as advocating the application of simple birth–death models, our goal here is to show how a particular model violation does not necessitate the abandonment of an entire field: use prudent caution, but do not abandon all hope.     

Northward shift in faunal diversity is a general pattern of evolution of the phanerozoic marine biota

The analysis of two global databases on spatio-temporal distribution of fossil marine animal genera (Sepkoski's compendium and The Paleobiology Database) has revealed the presence of the latitudinal diversity gradient (LDG) in the marine realm throughout the Phanerozoic. Within each time interval, LDG is characterized by two parameters: the latitudinal position of peak diversity and the steepness of monotonous decline of diversity with increasing distance from the zone of the highest diversity. During the Phanerozoic, peak diversity has drifted gradually from the tropics and subtropics of the Southern hemisphere into northern midlatitudes. The shift in peak diversity is not likely to be an artifact of incompleteness of the fossil record or uneven sampling of different regions. The shift proceeded in a stepwise manner, with periods of relatively fast changes separated by longer periods of little or no change. The latitudinal shift in peak diversity was probably due to a combination of several causes: tectonic (northward shift in the latitudinal distribution of continental shelf area), climatic (as demonstrated by the fact that peak diversity tended to occur near equator during the cold epochs and in midlatitudes during the warm epochs), and historical ("evolutionary inertia" of local faunas).     

Latitudinal diversity gradients for brachiopod genera during late Palaeozoic time: links between climate, biogeography and evolutionary rates

Aim The latitudinal diversity gradient, in which taxonomic richness is greatest at low latitudes and declines towards the poles, is a pervasive feature of the biota through geological time. This study utilizes fossil data to examine how the latitudinal diversity gradient and associated spatial patterns covaried through the major climate shifts at the onset and end of the late Palaeozoic ice age. Location Data were acquired from fossil localities from around the world. Methods Latitudinal patterns of diversity, mean geographical range size and macroevolutionary rates were constructed from a literature‐derived data base of occurrences of fossil brachiopod genera in space and time. The literature search resulted in a total of 18,596 occurrences for 991 genera from 2320 localities. Results Climate changes associated with the onset of the late Palaeozoic ice age (c. 327 Ma) altered the biogeographical structure of the brachiopod fauna by the preferential elimination of narrowly distributed, largely tropical genera when glaciation began. Because the oceans were left populated primarily with widespread genera, the slope of the diversity gradient became gentle at this time, and the gradient of average latitudinal range size weakened. In addition, because narrowly distributed genera had intrinsically high rates of origination and extinction, the gradients of both of these macroevolutionary rates were also reduced. These patterns were reversed when the ice age climate abated in early Permian time (c. 290 Ma): narrowly distributed genera rediversified at low latitudes, restoring steep gradients of diversity, average latitudinal range size and macroevolutionary rates. Main conclusions During late Palaeozoic time, these latitudinal gradients for brachiopods may have been linked by the increased magnitude of seasonality during the late Palaeozoic ice age. Pronounced seasonality would have prevented the existence of genera with narrow latitudinal ranges. These results for the late Palaeozoic ice age suggest a climatic basis for the present‐day latitudinal diversity gradient.     

gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth’s biodiversity

Understanding the origins of biodiversity has been an aspiration since the days of early naturalists. The immense complexity of ecological, evolutionary, and spatial processes, however, has made this goal elusive to this day. Computer models serve progress in many scientific fields, but in the fields of macroecology and macroevolution, eco-evolutionary models are comparatively less developed. We present a general, spatially explicit, eco-evolutionary engine with a modular implementation that enables the modeling of multiple macroecological and macroevolutionary processes and feedbacks across representative spatiotemporally dynamic landscapes. Modeled processes can include species’ abiotic tolerances, biotic interactions, dispersal, speciation, and evolution of ecological traits. Commonly observed biodiversity patterns, such as α, β, and γ diversity, species ranges, ecological traits, and phylogenies, emerge as simulations proceed. As an illustration, we examine alternative hypotheses expected to have shaped the latitudinal diversity gradient (LDG) during the Earth’s Cenozoic era. Our exploratory simulations simultaneously produce multiple realistic biodiversity patterns, such as the LDG, current species richness, and range size frequencies, as well as phylogenetic metrics. The model engine is open source and available as an R package, enabling future exploration of various landscapes and biological processes, while outputs can be linked with a variety of empirical biodiversity patterns. This work represents a key toward a numeric, interdisciplinary, and mechanistic understanding of the physical and biological processes that shape Earth’s biodiversity.

This study describes a novel mechanistic engine that predicts a realistic global latitudinal diversity gradient, species richness distribution and phylogenies. This approach is a step towards the interdisciplinary numeric understanding of the physical and biological processes that have shaped Earth’s biodiversity.     

A latitudinal gradient in rates of evolution of avian syllable diversity and song length

We ask whether rates of evolution in traits important for reproductive isolation vary across a latitudinal gradient, by quantifying evolutionary rates of two traits important for pre-mating isolation-avian syllable diversity and song length. We analyse over 2500 songs from 116 pairs of closely related New World passerine bird taxa to show that evolutionary rates for the two main groups of passerines-oscines and suboscines-doubled with latitude in both groups for song length. For syllable diversity, oscines (who transmit song culturally) evolved more than 20 times faster at high latitudes than in low latitudes, whereas suboscines (whose songs are innate in most species and who possess very simple song with few syllable types) show no clear latitudinal gradient in rate. Evolutionary rates in oscines and suboscines were similar at tropical latitudes for syllable complexity as well as for song length. These results suggest that evolutionary rates in traits important to reproductive isolation and speciation are influenced by latitude and have been fastest, not in the tropics where species diversity is highest, but towards the poles.     

Faster Speciation and Reduced Extinction in the Tropics Contribute to the Mammalian Latitudinal Diversity Gradient

The increase in species richness from the poles to the tropics, referred to as the latitudinal diversity gradient, is one of the most ubiquitous biodiversity patterns in the natural world. Although understanding how rates of speciation and extinction vary with latitude is central to explaining this pattern, such analyses have been impeded by the difficulty of estimating diversification rates associated with specific geographic locations. Here, we use a powerful phylogenetic approach and a nearly complete phylogeny of mammals to estimate speciation, extinction, and dispersal rates associated with the tropical and temperate biomes. Overall, speciation rates are higher, and extinction rates lower, in the tropics than in temperate regions. The diversity of the eight most species-rich mammalian orders (covering 92% of all mammals) peaks in the tropics, except that of the Lagomorpha (hares, rabbits, and pikas) reaching a maxima in northern-temperate regions. Latitudinal patterns in diversification rates are strikingly consistent with these diversity patterns, with peaks in species richness associated with low extinction rates (Primates and Lagomorpha), high speciation rates (Diprotodontia, Artiodactyla, and Soricomorpha), or both (Chiroptera and Rodentia). Rates of range expansion were typically higher from the tropics to the temperate regions than in the other direction, supporting the “out of the tropics” hypothesis whereby species originate in the tropics and disperse into higher latitudes. Overall, these results suggest that differences in diversification rates have played a major role in shaping the modern latitudinal diversity gradient in mammals, and illustrate the usefulness of recently developed phylogenetic approaches for understanding this famous yet mysterious pattern.     

Geographic signatures in species turnover: decoupling colonization and extinction across a latitudinal gradient

High latitude communities have low species richness and are rapidly warming with climate change. Thus, temporal changes in community composition are expected to be greatest at high latitudes. However, at the same time traits such as body size can also change with latitude, potentially offsetting or increasing changes to community composition over time. We tested how zooplankton communities (copepods and cladocerans) have changed over a 25–75 year time span by assessing colonization and extinction rates from lakes across an 1800 km latitudinal gradient, and further tested whether species traits predict rates of community change over time. Lake‐level dissimilarity, measured with Sorenson distance, decreased at higher latitudes. This decrease was due to higher colonization rates of cladocerans in lower latitude lakes and consistent extinction rates across the latitudinal gradient. At the species level, colonization increased with regional occupancy, and tended to be higher for smaller bodied, locally abundant, species. Local extinction rates were negatively correlated with local abundance and regional occupancy, but were not influenced by body size. None of these species‐specific characteristics changed predictably with latitude. Contrary to our expectations, low‐latitude zooplankton communities changed more rapidly than high‐latitude communities by becoming more species rich, not by losing species that were historically present. Moreover, colonization and extinction trends suggest that lakes have become increasingly dominated by species with smaller body sizes and that are already common locally and regionally. Together, these findings indicate that rates of species turnover in freshwater lakes across a latitudinal gradient are not predicted by rates of temperature change, but that turnover is nonetheless resulting in trait‐shifts that favour small, generalist species.     

Latitudinal‐diversity gradients can be shaped by biotic processes: new insights from an eco‐evolutionary model

The processes involved in shaping latitudinal‐diversity gradients (LDGs) have been a longstanding source of debate and research. Climatic, historical and evolutionary factors have all been shown to contribute to the formation of LDGs. However, meta‐analyses have shown that different clades have LDG slopes that may vary in more than one order of magnitude. Such large variation cannot be explained solely by climatic or historical factors (e.g. difference in surface area between temperate and tropical zones) given that all clades within a geographic region are subject to the same conditions. Therefore, biotic processes intrinsic to each taxonomic group could be relevant in explaining rate differences in diversity decline across latitudinal gradients among groups. In this study, we developed a model simulating multiple competing species subjected (or not) to a demographic Allee effect. We simulated the range expansion of these species across an environmental gradient to show how these two overlooked factors (competition and Allee effects) are capable of modulating LDGs. Allee effects resulted in a steeper LDG given a higher probability of local extinction and lower colonization capacity compared to species without Allee effects. Likewise, stronger competition also led to a steeper decline in species diversity compared to scenarios with weaker species antagonistic interactions. This pattern occurred mostly due to the strength of priority effects, wherein scenarios with strong competition, species that dispersed earlier in the landscape were able to secure many patches whereas late‐arriving species were progressively precluded from expanding their ranges. Overall, our results suggest that the effect of biotic processes in shaping macroecological patterns could be more important than it is currently appreciated.