scholarly journals Ecological and biogeographic drivers of biodiversity cannot be resolved using clade age-richness data

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Daniel L. Rabosky ◽  
Roger B. J. Benson
Keyword(s):  
Species Richness ◽  
Comparative Studies ◽  
Degrees Of Freedom ◽  
Predictive Ability ◽  
Inference Procedure ◽  
Diversification Rates ◽  
Evolutionary Diversification ◽  
Point Estimates ◽  
Extant Species ◽  
Single Clade

AbstractEstimates of evolutionary diversification rates – speciation and extinction – have been used extensively to explain global biodiversity patterns. Many studies have analyzed diversification rates derived from just two pieces of information: a clade’s age and its extant species richness. This “age-richness rate” (ARR) estimator provides a convenient shortcut for comparative studies, but makes strong assumptions about the dynamics of species richness through time. Here we demonstrate that use of the ARR estimator in comparative studies is problematic on both theoretical and empirical grounds. We prove mathematically that ARR estimates are non-identifiable: there is no information in the data for a single clade that can distinguish a process with positive net diversification from one where net diversification is zero. Using paleontological time series, we demonstrate that the ARR estimator has no predictive ability for real datasets. These pathologies arise because the ARR inference procedure yields “point estimates” that have been computed under a saturated statistical model with zero degrees of freedom. Although ARR estimates remain useful in some contexts, they should be avoided for comparative studies of diversification and species richness.

scholarly journals Geometric morphometric analysis of the pronotum and elytron in stag beetles: insight into its diversity and evolution

ZooKeys ◽  
2019 ◽  
Vol 833 ◽  
pp. 21-40
Author(s):  
Mengna Zhang ◽  
Yongying Ruan ◽  
Xia Wan ◽  
Yijie Tong ◽  
Xingke Yang ◽  
...  
Keyword(s):  
Species Richness ◽  
Morphometric Analysis ◽  
Morphological Diversity ◽  
Geometric Morphometric ◽  
Mahalanobis Distances ◽  
Evolutionary Diversification ◽  
Extant Species ◽  
History Of ◽  
Geometric Morphometric Analysis ◽  
Stag Beetles

Stag beetles (Coleoptera, Scarabaeoidea, Lucanidae) have received extensive attention from researchers in behavioral ecology and evolutionary biology. There have been no previous quantitative analyses, particularly using a geometric morphometric approach based on a large sample of data, to shed light on the morphological diversity and evolution of Lucanidae. Thoracic adaptation and ecological differentiation are intimately related, and the pronotum bears important muscles and supports the locomotion of prothoracic legs. The elytron is an autapomorphy of the Coleoptera. To reconstruct and visualize the patterns of evolutionary diversification and phylogenetic history of shape change, an ancestral groundplan can be reconstructed by mapping geometric morphometric data onto a phylogenetic tree. In this study, the morphologies of the pronotum and elytron in 1303 stag beetles (Lucanidae), including approximately 99.2% of all globally described species, were examined, thus revealing several aspects of morphological diversity and evolution. First, on the basis of geometric morphometric analysis, we found significant morphological differences in the pronotum or elytron between any two Lucanidae subfamilies. And we subsequently reconstructed the ancestral groundplans of the two structures in stag beetles and compared them with those of extant species (through cladistic and geometric morphometric methods). The ancestral groundplan of Lucanidae was found to be most similar to extant Nicagini in both the pronotum and elytron, according to Mahalanobis distances. Furthermore, we analyzed species richness and morphological diversity of stag beetles and the relationships between them and found that the two parameters were not always correlated. Aesalinae was found to be the most diverse subfamily in both the pronotum and elytron, despite its poor species richness, and the diversity of the pronotum or elytron was not superior in Lucaninae, despite its high species richness. Our study provides insights into the morphological variations and evolutionary history of the pronotum and elytron in four subfamilies of stag beetles, and it illuminates the relationship between morphological diversity and species richness. Intriguingly, our analysis indicates that morphological diversity and species richness are not always correlated. These findings may stimulate further studies in this field.

scholarly journals Diversification, sympatry, and the emergence of mega-diverse tropical assemblages

2017 ◽  
Author(s):  
Jacob B. Socolar ◽  
Alexander C. Lees
Keyword(s):  
Species Richness ◽  
Species Coexistence ◽  
Sympatric Species ◽  
Latitudinal Gradients ◽  
Evolutionary Patterns ◽  
Multiple Timescales ◽  
Diversification Rates ◽  
Evolutionary Diversification ◽  
Extinction Rates ◽  
High Diversity

ABSTRACTGeographic gradients in species richness, including latitudinal gradients, can arise from geographic variation in any of three mechanisms: the geologic age of habitats, net rates of evolutionary diversification, or rates of sympatry among diversifying lineages. Here we show that variation in rates of sympatry is a dominant force structuring geographic richness gradients in birds. Species-rich sites contain disproportionately high numbers of recently diverged sympatric species but contain lineages with slower-than-average diversification rates. The positive sympatry-diversity relationship consistently overwhelms the negative diversification-diversity relationship, particularly among high-diversity sites (>250 species). These patterns repeat across biomes and continents with striking regularity, and remain consistent across multiple timescales, including the recent evolutionary past. Biogeographic and evolutionary patterns in birds are consistent with a role for ecological conditions in promoting species coexistence, which allows sister species to co-occur and potentially lowers extinction rates.

scholarly journals Explaining large-scale patterns of vertebrate diversity

2015 ◽  
Vol 11 (7) ◽  
pp. 20150506 ◽  
Author(s):  
John J. Wiens
Keyword(s):  
Species Richness ◽  
Large Scale ◽  
Comparative Methods ◽  
Phylogenetic Comparative Methods ◽  
Metabolic Rates ◽  
Diversification Rates ◽  
Richness Patterns ◽  
Current Species

The major clades of vertebrates differ dramatically in their current species richness, from 2 to more than 32 000 species each, but the causes of this variation remain poorly understood. For example, a previous study noted that vertebrate clades differ in their diversification rates, but did not explain why they differ. Using a time-calibrated phylogeny and phylogenetic comparative methods, I show that most variation in diversification rates among 12 major vertebrate clades has a simple ecological explanation: predominantly terrestrial clades (i.e. birds, mammals, and lizards and snakes) have higher net diversification rates than predominantly aquatic clades (i.e. amphibians, crocodilians, turtles and all fish clades). These differences in diversification rates are then strongly related to patterns of species richness. Habitat may be more important than other potential explanations for richness patterns in vertebrates (such as climate and metabolic rates) and may also help explain patterns of species richness in many other groups of organisms.

scholarly journals Pre-Gondwanan-breakup origin ofBeauprea(Proteaceae) explains its historical presence in New Caledonia and New Zealand

2016 ◽  
Vol 2 (4) ◽  
pp. e1501648 ◽  
Author(s):  
Tianhua He ◽  
Byron B. Lamont ◽  
Bruno Fogliani
Keyword(s):  
Species Richness ◽  
New Zealand ◽  
New Caledonia ◽  
Phylogenetic Relations ◽  
Southeastern Australia ◽  
The Pacific ◽  
Extant Species ◽  
Historical Presence ◽  
Fossil Records ◽  
Transoceanic Dispersal

New Caledonia and New Zealand belong to the now largely submerged continent Zealandia. Their high levels of endemism and species richness are usually considered the result of transoceanic dispersal events followed by diversification after they re-emerged from the Pacific Ocean in the mid-Cenozoic. We explore the origin and evolutionary history ofBeauprea(Proteaceae), which is now endemic to New Caledonia but was once spread throughout eastern Gondwana, including New Zealand. We review the extensiveBeauprea-type pollen data in the fossil records and analyze the relationship of these fossil taxa to extant genera within Proteaceae. We further reconstruct the phylogenetic relations among nine extant species ofBeaupreaand estimate the age of theBeaupreaclade. By incorporating extinct taxa into theBeaupreaphylogenetic tree, we reconstruct the ancient distribution of this genus. Our analysis shows thatBeaupreaoriginated c. 88 Ma (million years ago) in Antarctica–Southeastern Australia and spread throughout Gondwana before its complete breakup. We propose thatBeauprea, already existing as two lineages, was carried with Zealandia when it separated from the rest of Gondwana c. 82 Ma, thus supporting an autochthonous origin forBeaupreaspecies now in New Caledonia and historically in New Zealand up to 1 Ma. We show that the presence ofBeaupreathrough transoceanic dispersal is implausible. This means that neither New Caledonia nor New Zealand has been entirely submerged since the Upper Cretaceous; thus, possible vicariance and allopatry must be taken into account when considering the high levels of endemism and species richness of these island groups.

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

2010 ◽  
Vol 277 (1700) ◽  
pp. 3587-3592 ◽  
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.

scholarly journals Diversification rates and species richness across the Tree of Life

2016 ◽  
Vol 283 (1838) ◽  
pp. 20161334 ◽  
Author(s):  
Joshua P. Scholl ◽  
John J. Wiens
Keyword(s):  
Species Richness ◽  
Positive Relationship ◽  
Tree Of Life ◽  
Diversification Rate ◽  
Substantial Variation ◽  
Diversification Rates ◽  
Higher Taxa ◽  
Over Time

Species richness varies dramatically among clades across the Tree of Life, by over a million-fold in some cases (e.g. placozoans versus arthropods). Two major explanations for differences in richness among clades are the clade-age hypothesis (i.e. species-rich clades are older) and the diversification-rate hypothesis (i.e. species-rich clades diversify more rapidly, where diversification rate is the net balance of speciation and extinction over time). Here, we examine patterns of variation in diversification rates across the Tree of Life. We address how rates vary across higher taxa, whether rates within higher taxa are related to the subclades within them, and how diversification rates of clades are related to their species richness. We find substantial variation in diversification rates, with rates in plants nearly twice as high as in animals, and rates in some eukaryotes approximately 10-fold faster than prokaryotes. Rates for each kingdom-level clade are then significantly related to the subclades within them. Although caution is needed when interpreting relationships between diversification rates and richness, a positive relationship between the two is not inevitable. We find that variation in diversification rates seems to explain most variation in richness among clades across the Tree of Life, in contrast to the conclusions of previous studies.

scholarly journals The Dynamics of Bird Diversity in the New World

2020 ◽  
Vol 69 (6) ◽  
pp. 1180-1199 ◽  
Author(s):  
Antonin Machac
Keyword(s):  
Species Richness ◽  
New World ◽  
Dominant Role ◽  
Bird Diversity ◽  
Biodiversity Hotspots ◽  
Relative Importance ◽  
Diversification Rates ◽  
The Andes ◽  
The Rich ◽  
Over Time

Abstract Three prominent explanations have been proposed to explain the dramatic differences in species richness across regions and elevations, (i) time for speciation, (ii) diversification rates, and (iii) ecological limits. But the relative importance of these explanations and, especially, their interplay and possible synthesis remain largely elusive. Integrating diversification analyses, null models, and geographic information systems, I study avian richness across regions and elevations of the New World. My results reveal that even though the three explanations are differentially important (with ecological limits playing the dominant role), each contributes uniquely to the formation of richness gradients. Further, my results reveal the likely interplay between the explanations. They indicate that ecological limits hinder the diversification process, such that the accumulation of species within a region gradually slows down over time. Yet, it does not seem to converge toward a hard ceiling on regional richness. Instead, species-rich regions show suppressed, but continued, diversification, coupled with signatures of possible competition (esp. Neotropical lowlands). Conversely, species-poor, newly-colonized regions show fast diversification and weak to no signs of competition (esp. Nearctic highlands). These results held across five families of birds, across grid cells, biomes, and elevations. Together, my findings begin to illuminate the rich, yet highly consistent, interplay of the mechanisms that together shape richness gradients in the New World, including the most species-rich biodiversity hotspots on the planet, the Andes and the Amazon. [Biogeography; community; competition; macroevolution; phylogenetics; richness gradient.]

scholarly journals Accelerated diversification correlated with functional traits shapes extant diversity of the early divergent angiosperm family Annonaceae

2019 ◽  
Author(s):  
B. Xue ◽  
X. Guo ◽  
J.B. Landis ◽  
M. Sun ◽  
C.C. Tang ◽  
...  
Keyword(s):  
Species Richness ◽  
Method Of Moments ◽  
Pollen Dispersal ◽  
Sex Expression ◽  
Diversification Rates ◽  
Total Species Richness ◽  
Dispersal Unit ◽  
High Species Richness ◽  
Selected Traits ◽  
Method Of Moments Estimator

BackgroundA major goal of phylogenetic systematics is to understand both the patterns of diversification and the processes by which these patterns are formed. Few studies have focused on the ancient, species-rich Magnoliales clade and its diversification pattern. Within Magnoliales, the pantropically distributed Annonaceae are by far the most genus-rich and species-rich family-level clade, with c. 110 genera and c. 2,400 species. We investigated the diversification patterns across Annonaceae and identified traits that show varied associations with diversification rates using a time-calibrated phylogeny of 835 species (34.6% sampling) and 11,211 aligned bases from eight regions of the plastid genome (rbcL, matK, ndhF, psbA-trnH, trnL-F, atpB-rbcL, trnS-G, and ycf1). Two hypotheses that might explain patterns of diversification—the ‘museum model’ and heterogeneous diversification rates—are also evaluated.ResultsTwelve rate shifts were identified using BAMM: in Annona, Artabotrys, Asimina, Drepananthus, Duguetia, Goniothalamus, Guatteria, Uvaria, Xylopia, the tribes Miliuseae and Malmeeae, and the Desmos-Dasymaschalon-Friesodielsia-Monanthotaxis clade (which collectively account for over 80% of the total species richness in the family). TurboMEDUSA and method-of-moments estimator analyses showed largely congruent results. A positive relationship between species richness and diversification rate is revealed using PGLS. We further explore the possible role of selected traits (habit, pollinator trapping, floral sex expression, pollen dispersal unit, anther septation, and seed dispersal unit) in shaping diversification patterns, based on inferences of BiSSE, MuSSE, HiSSE, and FiSSE analyses. Our results suggest that the liana habit, the presence of circadian pollinator trapping, androdioecy, and the dispersal of seeds as single-seeded monocarp fragments are closely correlated with higher diversification rates; pollen aggregation and anther septation, in contrast, are associated with lower diversification rates.ConclusionOur results show that the high species richness in Annonaceae is likely the result of recent increased diversification rather than the steady accumulation of species via the ‘museum model’. BAMM, turboMEDUSA, and the method-of-moments estimator all indicate heterogeneity in diversification rates across the phylogeny, with different traits associated with shifts in diversification rates in different Annonaceae clades.

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