Ecological causes of uneven speciation and species richness in mammals

ABSTRACTBiodiversity is distributed unevenly from the poles to the equator, and among branches of the tree of life, yet how those enigmatic patterns are related is unclear. We investigated global speciation-rate variation across crown Mammalia using a novel time-scaled phylogeny (N=5,911 species, ~70% with DNA), finding that trait- and latitude-associated speciation has caused uneven species richness among groups. We identify 24 branch-specific shifts in net diversification rates linked to ecological traits. Using time-slices to define clades, we show that speciation rates are a stronger predictor of clade richness than age. Speciation is slower in tropical than extra-tropical lineages, but only at the level of clades not species tips, consistent with fossil evidence that the latitudinal diversity gradient may be a relatively young phenomenon in mammals. In contrast, species tip rates are fastest in mammals that are low dispersal or diurnal, consistent with models of ephemeral speciation and ecological opportunity, respectively. These findings juxtapose nested levels of diversification, suggesting a central role of species turnover gradients in generating uneven patterns of modern biodiversity.

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Angiosperm speciation speeds up near the poles

10.1101/619064 ◽

2019 ◽

Cited By ~ 1

Author(s):

J. Igea ◽

A. J. Tanentzap

Keyword(s):

Species Richness ◽

Environmental Change ◽

Species Turnover ◽

Undescribed Species ◽

Opposite Pattern ◽

Speciation Rate ◽

Diversity Gradient ◽

Speciation Rates ◽

Angiosperm Species ◽

The Tropics

AbstractRecent evidence has questioned whether the Latitudinal Diversity Gradient (LDG), whereby species richness increases towards the Equator, results from higher rates of speciation in the tropics. Allowing for time heterogeneity in speciation rate estimates for over 60,000 angiosperm species, we found that the LDG does not arise from variation in speciation rates because lineages do not speciate faster in the tropics. These results were consistently retrieved using two other methods to test the association between occupancy of tropical habitats and speciation rates. Our speciation rate estimates were robust to the effects of both undescribed species and missing taxa. Overall, our results show that speciation rates follow an opposite pattern to global variation in species richness. Greater ecological opportunity in the temperate zones, stemming from less saturated communities, higher species turnover or greater environmental change, may ultimately explain these results.

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Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2010.0965 ◽

2010 ◽

Vol 277 (1700) ◽

pp. 3587-3592 ◽

Cited By ~ 91

Author(s):

Soo Hyung Eo ◽

J. Andrew DeWoody

Keyword(s):

Species Richness ◽

Nuclear Data ◽

Synonymous Substitution ◽

Evolutionary Rates ◽

Rate Variation ◽

Substitution Rates ◽

Diversification Rates ◽

Extinction Process ◽

Molecular Evolutionary Rates ◽

Speciation Rates

Rates of biological diversification should ultimately correspond to rates of genome evolution. Recent studies have compared diversification rates with phylogenetic branch lengths, but incomplete phylogenies hamper such analyses for many taxa. Herein, we use pairwise comparisons of confamilial sauropsid (bird and reptile) mitochondrial DNA (mtDNA) genome sequences to estimate substitution rates. These molecular evolutionary rates are considered in light of the age and species richness of each taxonomic family, using a random-walk speciation–extinction process to estimate rates of diversification. We find the molecular clock ticks at disparate rates in different families and at different genes. For example, evolutionary rates are relatively fast in snakes and lizards, intermediate in crocodilians and slow in turtles and birds. There was also rate variation across genes, where non-synonymous substitution rates were fastest at ATP8 and slowest at CO 3. Family-by-gene interactions were significant, indicating that local clocks vary substantially among sauropsids. Most importantly, we find evidence that mitochondrial genome evolutionary rates are positively correlated with speciation rates and with contemporary species richness. Nuclear sequences are poorly represented among reptiles, but the correlation between rates of molecular evolution and species diversification also extends to 18 avian nuclear genes we tested. Thus, the nuclear data buttress our mtDNA findings.

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Tip rates, phylogenies, and diversification: what are we estimating, and how good are the estimates?

10.1101/369124 ◽

2018 ◽

Cited By ~ 1

Author(s):

Pascal O. Title ◽

Daniel L. Rabosky

Keyword(s):

Diversification Rate ◽

Rate Variation ◽

Terminal Branch ◽

List Type ◽

Large Set ◽

Extinction Rate ◽

Diversification Rates ◽

Speciation Rate ◽

Model Based ◽

Model Free

AbstractSpecies-specific diversification rates, or “tip rates”, can be computed quickly from phylogenies and are widely used to study diversification rate variation in relation to geography, ecology, and phenotypes. These tip rates provide a number of theoretical and practical advantages, such as the relaxation of assumptions of rate homogeneity in trait-dependent diversification studies. However, there is substantial confusion in the literature regarding whether these metrics estimate speciation or net diversification rates. Additionally, no study has yet compared the relative performance and accuracy of tip rate metrics across simulated diversification scenarios.We compared the statistical performance of three model-free rate metrics (inverse terminal branch lengths; node density metric; DR statistic) and a model-based approach (BAMM). We applied each method to a large set of simulated phylogenies that had been generated under different diversification processes; scenarios included multi-regime time-constant and diversity-dependent trees, as well as trees where the rate of speciation evolves under a diffusion process. We summarized performance in relation to the type of rate variation, the magnitude of rate heterogeneity and rate regime size. We also compared the ability of the metrics to estimate both speciation and net diversification rates.We show decisively that model-free tip rate metrics provide a better estimate of the rate of speciation than of net diversification. Error in net diversification rate estimates increases as a function of the relative extinction rate. In contrast, error in speciation rate estimates is low and relatively insensitive to extinction. Overall, and in particular when relative extinction was high, BAMM inferred the most accurate tip rates and exhibited lower error than non-model-based approaches. DR was highly correlated with true speciation rates but exhibited high error variance, and was the best metric for very small rate regimes.We found that, of the metrics tested, DR and BAMM are the most useful metrics for studying speciation rate dynamics and trait-dependent diversification. Although BAMM was more accurate than DR overall, the two approaches have complementary strengths. Because tip rate metrics are more reliable estimators of speciation rate, we recommend that empirical studies using these metrics exercise caution when drawing biological interpretations in any situation where the distinction between speciation and net diversification is important.

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The latitudinal gradient in rates of evolution for bird beaks, a species interaction trait

10.1101/2020.07.31.231142 ◽

2020 ◽

Author(s):

Benjamin G Freeman ◽

Dolph Schluter ◽

Joseph A Tobias

Keyword(s):

Meta Analysis ◽

Biotic Interactions ◽

Species Interaction ◽

Temperate Zone ◽

Ecological Opportunity ◽

Evolutionary Diversification ◽

Diversity Gradient ◽

Rates Of Evolution ◽

Speciation Rates ◽

Beak Size

AbstractWhere is evolution fastest? The biotic interactions hypothesis proposes that greater species richness creates more ecological opportunity, driving faster evolution at low latitudes, whereas the “empty niches” hypothesis proposes that ecological opportunity is greater where diversity is low, spurring faster evolution at high latitudes. Here we tested these contrasting predictions by analyzing rates of bird beak evolution for a global dataset of 1141 sister pairs of birds. Beak size evolves at similar rates across latitudes, while beak shape evolves faster in the temperate zone, consistent with the empty niches hypothesis. We show in a meta-analysis that trait evolution and recent speciation rates are faster in the temperate zone, while rates of molecular evolution are slightly faster in the tropics. Our results suggest that drivers of evolutionary diversification are more potent at higher latitudes, thus calling into question multiple hypotheses invoking faster tropical evolution to explain the latitudinal diversity gradient.

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Polyploidy increases overall diversity despite higher turnover than diploids in the Brassicaceae

10.1101/717306 ◽

2019 ◽

Author(s):

Cristian Román-Palacios ◽

Y. Franchesco Molina-Henao ◽

Michael S. Barker

Keyword(s):

Species Richness ◽

Chromosome Numbers ◽

Long Term Evolution ◽

Tree Of Life ◽

Evolutionary Significance ◽

Diversification Rates ◽

Diversity Patterns ◽

Term Evolution ◽

Speciation Rates

AbstractAlthough polyploidy, or whole-genome duplication, is widespread across the Plant Tree of Life, its long-term evolutionary significance is still poorly understood. Here we examine the effects of polyploidy in driving macroevolutionary patterns within the angiosperm family Brassicaceae, a speciose clade exhibiting extensive inter-specific variation in chromosome numbers. We inferred ploidal levels from haploid chromosome numbers for 80% of species in the most comprehensive species-level chronogram for the Brassicaceae published to date. After evaluating a total of 54 phylogenetic models of diversification, we found that ploidy drives diversification rates across the Brassicaceae, with polyploids experiencing faster rates of speciation and extinction, but relatively slower rates of diversification. Nevertheless, diversification rates are, on average, positive for both polyploids and diploids. We also found that despite diversifying significantly slower than diploids, polyploids have played a significant role in driving present-day differences in species richness among clades. Overall, although most polyploids go extinct before sustainable populations are established, rare successful polyploids persist and significantly contribute to the long-term evolution of lineages. Our findings suggest that polyploidy has played a major role in shaping the long-term evolution of the Brassicaceae and highlight the importance of polyploidy in shaping present-day diversity patterns across the plant Tree of Life.Significance statementAlthough polyploidy is a source of innovation, its long-term evolutionary significance is still debated. Here we analyze the evolutionary role of polyploidy within the Brassicaceae, a diverse clade exhibiting extensive variation in chromosome numbers among species. We found that, although polyploids diversify slower than diploids, polyploids have faster extinction and speciation rates. Our results also suggest that polyploidy has played an important role in shaping present-day differences in species richness within the Brassicaceae, with potential implications in explaining diversity patterns across the plant Tree of Life.

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The contribution of global mountains to the latitudinal diversity gradient

10.1101/2020.07.04.188227 ◽

2020 ◽

Author(s):

Elkin A. Tenorio ◽

Paola Montoya ◽

Natalia Norden ◽

Susana Rodríguez-Buriticá ◽

Beatriz Salgado-Negret ◽

...

Keyword(s):

Species Richness ◽

Unit Area ◽

Species Turnover ◽

Geographical Information ◽

Mountain Ranges ◽

Terrestrial Vertebrates ◽

Latitudinal Diversity Gradient ◽

Diversity Gradient ◽

Diversity Gradients ◽

Time And Energy

AbstractThe latitudinal diversity gradient (LDG) is widely attributed to be the result of factors such as time, area, and energy. Although these factors explain most of the variation in lowlands, they fail in mountainous systems, which are biodiversity hotspots that may contribute meaningfully to the strength of the pattern following different evolutionary pathways. However, because lowlands cover the largest portion of the total land, they may have overshadowed the contribution of mountains to the LDG, but no study has addressed this issue in previous macroecological analyses. Here, we propose that the LDG shows a stronger trend in mountain ranges due to their high species turnover, in spite of covering less than one third of the Earth’s land. Using the geographical information for ∼22000 species of terrestrial vertebrates, we show that worldwide mountains harbor the 40% of the global diversity, and when taking into account the area effect, we quantified that mountains harbor close to double the species inhabiting lowlands per unit area. Moreover, when we evaluated the LDG after accounting for area size, we found that species richness increased faster towards the Equator and was better predicted by latitude in mountains than in lowlands. Our findings challenge previously well-supported hypotheses that predict that those regions with greater area, time and energy accumulate more species richness, since mountains are geologically younger, exhibit less energy, and cover smaller areas than lowlands. Hence, mountains represent a paradox, which invites to reevaluate hypotheses regarding macroecological and evolutionary processes driving species diversity gradients.

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Earth history events shaped the evolution of uneven biodiversity across tropical moist forests

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2026347118 ◽

2021 ◽

Vol 118 (40) ◽

pp. e2026347118 ◽

Cited By ~ 1

Author(s):

Oskar Hagen ◽

Alexander Skeels ◽

Renske E. Onstein ◽

Walter Jetz ◽

Loïc Pellissier

Keyword(s):

Species Richness ◽

Terrestrial Plants ◽

Spatially Explicit Model ◽

Deep Time ◽

Extinction Rates ◽

Speciation Rates ◽

Tectonic Reconstructions ◽

The Relationship ◽

Contemporary Climate

Far from a uniform band, the biodiversity found across Earth’s tropical moist forests varies widely between the high diversity of the Neotropics and Indomalaya and the relatively lower diversity of the Afrotropics. Explanations for this variation across different regions, the “pantropical diversity disparity” (PDD), remain contentious, due to difficulty teasing apart the effects of contemporary climate and paleoenvironmental history. Here, we assess the ubiquity of the PDD in over 150,000 species of terrestrial plants and vertebrates and investigate the relationship between the present-day climate and patterns of species richness. We then investigate the consequences of paleoenvironmental dynamics on the emergence of biodiversity gradients using a spatially explicit model of diversification coupled with paleoenvironmental and plate tectonic reconstructions. Contemporary climate is insufficient in explaining the PDD; instead, a simple model of diversification and temperature niche evolution coupled with paleoaridity constraints is successful in reproducing the variation in species richness and phylogenetic diversity seen repeatedly among plant and animal taxa, suggesting a prevalent role of paleoenvironmental dynamics in combination with niche conservatism. The model indicates that high biodiversity in Neotropical and Indomalayan moist forests is driven by complex macroevolutionary dynamics associated with mountain uplift. In contrast, lower diversity in Afrotropical forests is associated with lower speciation rates and higher extinction rates driven by sustained aridification over the Cenozoic. Our analyses provide a mechanistic understanding of the emergence of uneven diversity in tropical moist forests across 110 Ma of Earth’s history, highlighting the importance of deep-time paleoenvironmental legacies in determining biodiversity patterns.

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Ecological Specialization and Diversification in Birds

10.1101/2020.06.13.142703 ◽

2020 ◽

Author(s):

Nicholas M. A. Crouch ◽

Robert E. Ricklefs ◽

Boris Igić

Keyword(s):

Species Richness ◽

Ecological Specialization ◽

Diversification Rates ◽

Speciation Rate ◽

Extinction Rates ◽

Allopatric Species ◽

Species Formation ◽

Geographic Distributions ◽

Local Ecology ◽

Lineage Diversification

AbstractEcological specialization is widely thought to influence patterns of species richness by affecting rates at which species multiply and perish. Quantifying specialization is challenging, and using only one or a small number of ecological axes could bias estimates of overall specialization. Here, we calculate an index of specialization, based on seven measured traits, and estimate its effect on speciation and extinction rates in a large clade of birds. We find that speciation rate is independent of specialization, suggesting independence of local ecology and the geographic distributions of populations that promote allopatric species formation. Although some analyses suggest that more specialized species have higher extinction rates, leading to negative net diversification, this relationship is not consistently identified across our analyses. Our results suggest that specialization may drive diversification dynamics only on local scales or in specific clades, but is not generally responsible for macroevolutionary disparity in lineage diversification rates.

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Fast diversification through a mosaic of evolutionary histories characterizes the endemic flora of ancient Neotropical mountains

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2019.2933 ◽

2020 ◽

Vol 287 (1923) ◽

pp. 20192933 ◽

Cited By ~ 10

Author(s):

Thais N. C. Vasconcelos ◽

Suzana Alcantara ◽

Caroline O. Andrino ◽

Félix Forest ◽

Marcelo Reginato ◽

...

Keyword(s):

Species Richness ◽

Plant Species ◽

Species Turnover ◽

Plant Species Richness ◽

Campo Rupestre ◽

Population Isolation ◽

Mountain Ranges ◽

Extinction Rates ◽

Speciation Rates ◽

Endemic Flora

Mountains are among the most biodiverse areas on the globe. In young mountain ranges, exceptional plant species richness is often associated with recent and rapid radiations linked to the mountain uplift itself. In ancient mountains, however, orogeny vastly precedes the evolution of vascular plants, so species richness has been explained by species accumulation during long periods of low extinction rates. Here we evaluate these assumptions by analysing plant diversification dynamics in the campo rupestre , an ecosystem associated with pre-Cambrian mountaintops and highlands of eastern South America, areas where plant species richness and endemism are among the highest in the world. Analyses of 15 angiosperm clades show that radiations of endemics exhibit fastest rates of diversification during the last 5 Myr, a climatically unstable period. However, results from ancestral range estimations using different models disagree on the age of the earliest in situ speciation events and point to a complex floristic assembly. There is a general trend for higher diversification rates associated with these areas, but endemism may also increase or reduce extinction rates, depending on the group. Montane habitats, regardless of their geological age, may lead to boosts in speciation rates by accelerating population isolation in archipelago-like systems, circumstances that can also result in higher extinction rates and fast species turnover, misleading the age estimates of endemic lineages.

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The role of hummingbirds in the evolution and diversification of Bromeliaceae: unsupported claims and untested hypotheses

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boz100 ◽

2019 ◽

Vol 192 (4) ◽

pp. 592-608 ◽

Cited By ~ 3

Author(s):

Michael Kessler ◽

Stefan Abrahamczyk ◽

Thorsten Krömer

Keyword(s):

Underlying Mechanism ◽

Flowering Phenology ◽

Population Fragmentation ◽

Diversification Rates ◽

Pollen Transfer Efficiency ◽

Hummingbird Pollination ◽

Speciation Rates ◽

Plant Families ◽

C 32

Abstract At least half of the 3600 species of Bromeliaceae are pollinated by hummingbirds. There is little doubt that the four to 12 evolutionary shifts towards and c. 32 shifts away from hummingbird pollination opened new evolutionary spaces for bromeliad diversification, and that hummingbird pollination has led to increased bromeliad diversification rates. However, the mechanisms leading to these increased rates remain unclear. We here propose that there are four main types of mechanisms that may increase diversification rates of hummingbird-pollinated bromeliad clades: (1) bromeliad speciation through adaptation to different hummingbird species; (2) increased allopatric speciation in hummingbird-pollinated clades due to lower pollen transfer efficiency compared with other pollinators; (3) differential speciation rates in hummingbird-pollinated clades dependent on of flowering phenology and hummingbird behaviour; and (4) higher speciation rates of bromeliads in montane environments (where hummingbird pollination predominates) due to topographic population fragmentation. To date, none of these hypotheses has been appropriately tested, partly due to a lack of data, but also because research so far has focused on documenting the pattern of increased diversification in hummingbird-pollinated clades, implicitly assuming that this pattern supports an underlying mechanism while ignoring the fact that several competing mechanisms may be considered. The aim of the present review is to increase awareness of these mechanisms and to trigger research aimed at specifically testing them. We conclude that much additional research on the roles of hummingbird behaviour and gene flow between bromeliad species is needed to elucidate their contribution to the evolution of diversity in bromeliads and other plant families.

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