Rates Of Species Diversification Research Articles

Eco-evolutionary evidence for the global diversity pattern of Cycas (Cycadaceae).

The evolution of the latitudinal diversity gradient (LDG), characterized by a peak in diversity toward the tropics, has captured significant attention in evolutionary biology and ecology. However, the inverse LDG (i-LDG) mechanism, wherein species richness increases toward the poles, remains inadequately explored. Cycads are among one of the oldest lineages of extant seed plants and have undergone extensive diversification in the tropics. Intriguingly, the extant cycad abundance exhibits an i-LDG pattern, and the underlying causes for this phenomenon remain largely elusive. Here, using 1,843 nuclear genes from a nearly complete sampling, we conducted comprehensive phylogenomic analyses to establish a robust species-level phylogeny for Cycas, the largest genus within cycads. We then reconstructed the spatial-temporal dynamics and integrated global environmental data to evaluate the roles of species ages, diversification rates, contemporary environment, and conservatism to ancestral niches in shaping the i-LDG pattern. We found Cycas experienced decreased diversification rates, coupled with the cooling temperature since its origin in the Eocene from continental Asia. Different regions have distinctively contributed to the formation of i-LDG for Cycas, with the northern hemisphere acting as evolutionary museums and the southern hemisphere serving as cradles. Moreover, water-related climate variables, specifically precipitation seasonality and potential evapotranspiration, were identified as paramount factors constraining Cycas species richness in the rainforest biome near the equator. Notably, the adherence to ancestral monsoonal climates emerges as a critical factor in sustaining the diversity pattern. This study underscores the imperative of integrating both evolutionary and ecological approaches to comprehensively unravel the mechanisms underpinning global biodiversity patterns.

The relationship between geographic range size and rates of species diversification

Range size is a universal characteristic of every biological species, and is often assumed to affect diversification rate. There are strong theoretical arguments that large-ranged species should have higher rates of diversification. On the other hand, the observation that small-ranged species are often phylogenetically clustered might indicate high diversification of small-ranged species. This discrepancy between theory and the data may be caused by the fact that typical methods of data analysis do not account for range size changes during speciation. Here we use a cladogenetic state-dependent diversification model applied to mammals to show that range size changes during speciation are ubiquitous and small-ranged species indeed diversify generally slower, as theoretically expected. However, both range size and diversification are strongly influenced by idiosyncratic and spatially localized events, such as colonization of an archipelago or a mountain system, which often override the general pattern of range size evolution.

Climatic niche evolution in Smilacaceae (Liliales) drives patterns of species diversification and richness between the Old and New World

AbstractGeographical variation in species richness in plant groups is determined by the interplay between historical, evolutionary, and ecological processes. However, the processes underlying the striking disparity in species richness between Asia and the Americas remain poorly understood. Here, we synthesize global phylogenetic and macroecological data on the diversification of Smilacaceae, deciphering potential drivers underlying the species diversity pattern biased toward Asia. We compiled global distributions of all Smilacaceae species, and reconstructed the biogeographic history and niche evolution using a new time‐calibrated phylogeny (eight genes, 135 species). Integrating these data sets, we estimated evolutionary histories and diversification rates for each region, and tested correlations among species diversification, niche evolution, and niche divergence. Smilacaceae probably originated during the Late Cretaceous/Early Palaeocene and began to diversify in middle to low latitudes in Central America and Eurasia during the Late Eocene. Both the Old and New World clades exhibited a steady, albeit slight, increase of species diversification from the Late Eocene to Early Miocene. However, the Old World clade experienced an abrupt increase in net diversification during the Late Miocene. Our findings also revealed that species diversification rates were positively correlated with ecological niche evolution and niche divergence. Niche shifts and climatic niche evolution since the Middle Miocene played crucial roles in species diversification dynamics within Smilacaceae. The high plant richness in Asia may be explained by greater diversification in this region, potentially promoted by heterogeneous environments.

Chemical signaling glands are unlinked to species diversification in lizards.

Sexual selection has long been thought to increase species diversification. Sexually selected traits, such as sexual signals that contribute to reproductive isolation, were thought to promote diversification. However, studies exploring links between sexually selected traits and species diversification have thus far primarily focused on visual or acoustic signals. Many animals often employ chemical signals (i.e., pheromones) for sexual communications, but large-scale analyses on the role of chemical communications in driving species diversification have been missing. Here, for the first time, we investigate whether traits associated with chemical communications-the presence of follicular epidermal glands-promote diversification across 6,672 lizard species. In most analyses, we found no strong association between the presence of follicular epidermal glands and species diversification rates, either across all lizard species or at lower phylogenetic scales. Previous studies suggest that follicular gland secretions act as species recognition signals that prevent hybridization during speciation in lizards. However, we show that geographic range overlap was no different in sibling species pairs with and without follicular epidermal glands. Together, these results imply that either follicular epidermal glands do not primarily function in sexual communications or sexually selected traits in general (here chemical communication) have a limited effect on species diversification. In our additional analysis accounting for sex-specific differences in glands, we again found no detectable effect of follicular epidermal glands on species diversification rates. Thus, our study challenges the general role of sexually selected traits in broad-scale species diversification patterns.

Net diversification rates of the woody plant genus Petalidium (Acanthaceae) are highest in the ancient and arid Namib Desert

At present, tropical arid biomes house less woody plant species diversity than tropical moist biomes, which could be due to lower rates of evolutionary diversification in the recent or distant past. Here, we study the evolutionary diversification of Petalidium (Acanthaceae), a genus of 36 species of woody shrubs found in the Namib Desert of southwest Africa, and surrounding areas. We generated a new, nearly fully sampled and temporally calibrated phylogeny for Petalidium using RADseq SNP data and secondary calibrations. We then investigated variation in net diversification rate across the phylogeny, the ancestral climatic niche of lineages and the link between the two. We find that arid climatic conditions are linked with increased rates of net species diversification in the genus. Despite its great age, the Namib Desert clearly hosts young plant radiations. This apparent contradiction can be explained by a scenario of high evolutionary turnover, in this case potentially caused by alternating hyper-arid and relatively mesic phases. Hyper-arid phases could result in high plant mortality and extinction of species, leading to ecological opportunity and diversification during mesic phases. Taken together, our results contribute to a growing body of literature that shows evidence for elevated rates of plant diversification in the Quaternary in arid biomes across the globe.

Seed dormancy in Asteraceae: a global vegetation zone and taxonomic/phylogenetic assessment

AbstractThe Asteraceae with up to 30,000 species occurs on all continents except Antarctica and in all major vegetation zones on earth. Our primary aim was to consider cypselae dormancy-break and germination of Asteraceae in relation to ecology, vegetation zones and evolution. Cypselae are desiccation-tolerant and in various tribes, genera, species and life forms of Asteraceae are either non-dormant (ND) or have non-deep physiological dormancy (PD) at maturity. All six types of non-deep PD are found among the Asteraceae, and dormancy is broken by cold or warm stratification or by afterripening. Soil cypselae banks may be formed but mostly are short-lived. Much within-species variation in dormancy-break and germination has been found. Using data compiled for 1192 species in 373 genera and 35 tribes of Asteraceae, we considered ND and PD in relation to life form, vegetation zone and tribe. Senecioneae and Astereae had the best representation across the vegetation zones on earth. In evergreen and semi-evergreen rainforests, more species have ND than PD, but in all other vegetation zones, except alpine/high-latitude tundra (where ND and PD are equal), more species have PD than ND. Tribes in the basal and central grades and those in the Heliantheae Alliance have both ND and PD. The high diversity and lability of non-deep PD may have enhanced the rate of species diversification by promoting the survival of new species and/or species in new habitats that became available following globally disruptive events since the origin of the Asteraceae in the Late Cretaceous.

Aphid male wing polymorphisms are transient and have evolved repeatedly.

Polymorphic phenotypes have long been used to examine the maintenance of genetic variation within and between species. Most studies have focused on persistent polymorphisms, which are retained across species boundaries, and their positive effects on speciation rates. Far less is known about the macroevolutionary impacts of more transient polymorphisms, which are also common. Here we investigated male wing polymorphisms in aphids. We estimated the phylogenetic history of wing states across species, along with several other traits that could affect wing evolution. We found that male wing polymorphisms are transient: they are found in only ~4% of extant species, but have likely evolved repeatedly across the phylogeny. We reason that the repeated evolution of transient polymorphisms might be facilitated by the existence of the asexual female wing plasticity, which is common across aphids, and would maintain the wing development program even in species with wingless males. We also discovered that male wingedness correlates positively with host plant alternation and host plant breadth, and that winged morphs and wing polymorphisms may be associated with higher speciation rates. Our results provide new evolutionary insights into this well-studied group and suggest that even transient polymorphisms may impact species diversification rates.

Karyotypic diversity: a neglected trait to explain angiosperm diversification?

Evolutionary changes in karyotype provide genetic support to organisms' differentiation and adaptation; however, the association between karyotype diversity and species diversification in flowering plants (angiosperms) remains to be fully elucidated. We sought evidence for this association within a phylogenetic framework using a dataset comprising > 413,000 worldwide chromosome counts of 66,000 angiosperms species. Karyotypic diversity (e.g., number of distinct chromosome numbers) explains species richness and diversification rates at both family and genus levels highlighting that chromosome evolution has probably played, at least, an important role in reinforcing speciation that was already initiated or completed by other geographical or ecological drivers. Thus, research programs investigating chromosome variation as a direct or indirect driver of diversification should be encouraged.

Island life accelerates geographic radiation in the white‐eyes (Zosteropidae)

White‐eyes are an iconic avian radiation of small passerines that are mainly distributed across the eastern hemisphere tropics and subtropics. Species diversity of white‐eyes is particularly high on oceanic islands, and many species are restricted to single islands or island groups. The high rate of species diversification of white‐eyes ranks them among the fastest radiations known in birds, but whether their accelerated diversification was the result of repeatedly colonizing islands remains unexplored. We used a newly estimated timetree for nearly all zosteropids and phylogenetic comparative methods to estimate and compare diversification rates between island and continental lineages. We show that island white‐eyes have similar extinction rates, yet higher speciation rates compared with continental white‐eyes. In addition, we find higher rates of transitions from islands to continents. Our results show the importance of islands, such as Wallacean and Melanesian archipelagos of the Indo‐Pacific, in facilitating high rates of speciation within this remarkable clade.

The evolutionary rate of leaf osmotic strength drives diversification ofPrimulinaspecies in karst regions

AbstractLeaf water storage capacity and osmotic strength are important traits enabling species to adapt to environments that are often moisture limited. However, whether these drought tolerance traits are correlated with the species diversification rate (DR) of plant lineages is yet to be determined. In this study, we selected a species‐rich genus (Primulina) of plants widely distributed in karst regions in which species frequently experience variable periods of drought. We measured water storage capacity‐related traits (including leaf thickness and water content per mass) and saturated osmotic strength in the leaves of 58Primulinaspecies growing in a common garden. Subsequently, using phylogenetic methods, we examined the relationships between the rate of species diversification and the drought tolerance traits and between the species DR and evolutionary rates of these traits. We found that neither water storage capacity nor saturated osmotic strength showed significant relationships with the rate of species diversification. However, the evolutionary rate of saturated osmotic strength showed a significant correlation with the species DR, although no comparable significant relationship was detected regarding the evolutionary rate of water storage capacity. Our study indicates that the diversification amongPrimulinaspecies has typically been accompanied by an extensive divergence of leaf osmotic strength but not a divergence in leaf water storage capacity. These findings will enhance our current understanding of how drought tolerance influences the diversification of plant species in karst regions.

Defensive spines are associated with large geographic range but not diversification in spiny ants (Hymenoptera: Formicidae: Polyrhachis)

AbstractSeveral prominent evolutionary theories propose mechanisms whereby the evolution of a defensive trait or suite of traits causes significant shifts in species diversification rate and niche evolution. We investigate the role of cuticular spines, a highly variable morphological defensive trait in the hyperdiverse ant genus Polyrhachis, on species diversification and geographic range size. Informed by key innovation theory and the escape‐and‐radiate hypothesis, we predicted that clades with longer spines would exhibit elevated rates of diversification and larger range sizes compared to clades with shorter spines. To address these predictions, we estimated phylogenetic relationships with a phylogenomic approach utilizing ultraconserved elements and compiled morphological and biogeographic trait databases. In contrast to the first prediction, we found no association between diversification rate and any trait (spine length, body size and range size), with the sole exception of a positive association between range size and diversification in one of three trait‐based diversification analyses. However, we recovered a positive phylogenetic correlation between spine length and geographic range size, suggesting that spines promote expanded geographic range. Notably, these results were consistent across analyses using different phylogenetic inference approaches and spine trait measurement schemes. This study provides a rare investigation of the role of a defensive trait on geographic range size, and ultimately supports the hypothesis that defensive spines are a factor in increased range size in Polyrhachis ants. Furthermore, the lack of support for an association between spines and diversification, which contrasts with previous work demonstrating a positive association between spines and diversification rate, is intriguing and warrants further study.

Mito-nuclear selection induces a trade-off between species ecological dominance and evolutionary lifespan.

Mitochondrial and nuclear genomes must be co-adapted to ensure proper cellular respiration and energy production. Mito-nuclear incompatibility reduces individual fitness and induces hybrid infertility, which can drive reproductive barriers and speciation. Here, we develop a birth-death model for evolution in spatially extended populations under selection for mito-nuclear co-adaptation. Mating is constrained by physical and genetic proximity, and offspring inherit nuclear genomes from both parents, with recombination. The model predicts macroscopic patterns including a community's species diversity, species abundance distribution, speciation and extinction rates, as well as intraspecific and interspecific genetic variation. We explore how these long-term outcomes depend upon the parameters of reproduction: individual fitness governed by mito-nuclear compatibility, constraints on mating compatibility and ecological carrying capacity. We find that strong selection for mito-nuclear compatibility reduces the equilibrium number of species after a radiation, increasing species' abundances and simultaneously increasing both speciation and extinction rates. The negative correlation between species diversity and diversification rates in our model agrees with the broad empirical pattern of lower diversity and higher speciation/extinction rates in temperate regions, compared to the tropics. We conclude that these empirical patterns may be caused in part by latitudinal variation in metabolic demands and corresponding variation in selection for mito-nuclear function.

A study of the chromosome number and genome size of the rare species Rhododendron keiskei var. hypoglaucum in Korea

Rhododendron keiskei var. hypoglaucum (Ericaceae) was recently reported in Korea, with a disjunct distribution on the southern islands of the Korean Peninsula. Although chromosome numbers and ploidy variations are important traits in angiosperms, gaining a clear understanding the cytological features of Rhododendron has been hampered by the small size of its chromosomes. We herein report the chromosome number, karyotype structure, and genome size of R. keiskei var. hypoglaucum for the first time. The chromosome number of the investigated plants was 2n = 26 with x = 13 as the base chromosome number, which is the one of the frequently encountered base chromosome numbers in Rhododendron. The karyotype of R. keiskei var. hypoglaucum is composed of metacentric and submetacentric chromosomes similar in length, which ranged from 1.39 to 2.40 μm. The DNA 1C-value in all examined accessions was small, ranging from 0.63 to 0.65 pg, further supporting the stable genome size in Rhododendron. These comprehensive cytological results provide a framework for detailed molecular, cytogenetic, and phylogenomic analyses that can be used to interpret the slow species diversification rate in Rhododendron.

Global variation in diversification rate and species richness are unlinked in plants

Species richness varies immensely around the world. Variation in the rate of diversification (speciation minus extinction) is often hypothesized to explain this pattern, while alternative explanations invoke time or ecological carrying capacities as drivers. Focusing on seed plants, the world's most important engineers of terrestrial ecosystems, we investigated the role of diversification rate as a link between the environment and global species richness patterns. Applying structural equation modeling to a comprehensive distribution dataset and phylogenetic tree covering all circa 332,000 seed plant species and 99.9% of the world's terrestrial surface (excluding Antarctica), we test five broad hypotheses postulating that diversification serves as a mechanistic link between species richness and climate, climatic stability, seasonality, environmental heterogeneity, or the distribution of biomes. Our results show that the global patterns of species richness and diversification rate are entirely independent. Diversification rates were not highest in warm and wet climates, running counter to the Metabolic Theory of Ecology, one of the dominant explanations for global gradients in species richness. Instead, diversification rates were highest in edaphically diverse, dry areas that have experienced climate change during the Neogene. Meanwhile, we confirmed climate and environmental heterogeneity as the main drivers of species richness, but these effects did not involve diversification rates as a mechanistic link, calling for alternative explanations. We conclude that high species richness is likely driven by the antiquity of wet tropical areas (supporting the "tropical conservatism hypothesis") or the high ecological carrying capacity of warm, wet, and/or environmentally heterogeneous environments.

Macroevolutionary Analyses Provide New Evidence of Phasmid Wings Evolution as a Reversible Process

The concept that complex ancestral traits can never be recovered after their loss is still widely accepted, despite phylogenetic and molecular approaches suggest instances where phenotypes may have been lost throughout the evolutionary history of a clade and subsequently reverted back in derived lineages. One of the first and most notable examples of such a process is wing evolution in phasmids; this polyneopteran order of insects, which comprises stick and leaf insects, has played a central role in initiating a long-standing debate on the topic. In this study, a novel and comprehensive time tree including over 300 Phasmatodea species is used as a framework for investigating wing evolutionary patterns in the clade. Despite accounting for several possible biases and sources of uncertainty, macroevolutionary analyses consistently revealed multiple reversals to winged states taking place after their loss, and reversibility is coupled with higher species diversification rates. Our findings support a loss of or reduction in wings that occurred in the lineage leading to the extant phasmid most recent common ancestor, and brachyptery is inferred to be an unstable state unless co-opted for nonaerodynamic adaptations. We also explored how different assumptions of wing reversals probability could impact their inference: we found that until reversals are assumed to be over 30 times more unlikely than losses, they are consistently inferred despite uncertainty in tree and model parameters. Our findings demonstrate that wing evolution is a reversible and dynamic process in phasmids and contribute to our understanding of complex trait evolution. [Dollo's law; Phasmatodea; phylogenetic comparative methods; polyneoptera; reversals; wing.].

Linking the evolution of development of stem vascular system in Nyctaginaceae and its correlation to habit and species diversification

Background Alternative patterns of secondary growth in stems of Nyctaginaceae is present in all growth habits of the family and have been known for a long time. However, the interpretation of types of cambial variants have been controversial, given that different authors have given them different developmental interpretations. The different growth habits coupled with an enormous stem anatomical diversity offers the unique opportunity to investigate the evolution of complex developments, to address how these anatomies shifted within habits, and how the acquisition of novel cambial variants and habit transitions impacted the diversification of the family.MethodsWe integrated developmental data with a phylogenetic framework to investigate the diversity and evolution of stem anatomy in Nyctaginaceae using phylogenetic comparative methods, reconstructing ancestral states, and examining whether anatomical shifts correspond to species diversification rate shifts in the family.ResultsTwo types of cambial variants, interxylary phloem and successive cambia, were recorded in Nyctaginaceae, which result from four different ontogenies. These ontogenetic trajectories depart from two distinct primary vascular structures (regular or polycyclic eustele) yet, they contain shared developmental stages which generate stem morphologies with deconstructed boundaries of morphological categories (continuum morphology). Unlike our a priori hypotheses, interxylary phloem is reconstructed as the ancestral character for the family, with three ontogenies characterized as successive cambia evolving in few taxa. Cambial variants are not contingent on habits, and their transitions are independent from species diversification.ConclusionsOur findings suggest that multiple developmental mechanisms, such as heterochrony and heterotopy, generate the transitions between interxylary phloem and successive cambia. Intermediate between these two extremes are present in Nyctaginaceae, suggesting a continuum morphology across the family as a generator of anatomical diversity.

Basal phylogenetic asymmetry in species-rich natural taxa of plants: a multivariate study

Sister groups at the root of large plant clades (with ≥1000 extant species) are described in terms of variables expressing species richness, geographical distribution, age, diversification rate and speed of molecular evolution. Standard statistical tools and principal component analysis are used to determine and visualize their relationships. In the majority of the 167 groups examined, one clade (the minor) has many fewer species than its sister (the major clade). A striking phenomenon is that many minor clades (17%) contain four or fewer species only. Asymmetry is largely, but not generally reflected by proportions in geographical range and relative speed of molecular evolution: species in the minor clade are more widely distributed than the major clade in 8 groups and – based on available information – we detected longer maximum branch lengths on the minor lineage in 14 cases. The basal lineages considerably differ in diversification rate; the differences are of the same magnitude in many groups as the diversification rate itself calculated for families and orders by other authors. For the major clade, we found a positive relationship between the species richness of clades and geographical range, and negative correlation between the logarithm of species richness and clade age.

Molecular and phytochemical variability among genus Albizia: a phylogenetic prospect for future breeding.

Fabaceae, the third-largest Angiosperm family, exhibits great morphological diversity with significantly high species diversification rate. Albizia, one of the largest genera of the legume family, possesses high ecological, economical and medicinal application prospects and displays a global distribution. The taxonomic classification among Albizia remains, however, unclear and has been subjected to changes. The resolution of phylogenetic relationships among members of genus Albizia is a priority. Nine Albizia species cultivated in Egypt; Albizia lebbeck, A. julibrissin, A. odoratissima, A. procera, A. anthelmintica, A. guachapele, A. myriophylla, A. richardiana and A. lucida were subjected to molecular classification via DNA fingerprinting techniques viz. Inter Simple Sequence Repeat (ISSR) and Start Codon Targeted polymorphism (SCoT) using ten primers, five for each technique. The total number of bands produced by ISSR and SCoT primers was 28 and 40, respectively. The percentage of polymorphism varied from 64.28% in ISSR to 67.50% in SCoT analysis. Additionally, chemotaxonomic analysis was implemented based on UV spectroscopic profiling and total phenolic content coupled to unsupervised chemometric tools; Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA). Interspecific relationships were confirmed via molecular and phytochemical analyses between A. procera and A. guachapele; A. lebbeck and A. odoratissima; and A. julibrissin and A. lucida. The study reveals that chemotaxonomic data can reflect phylogenetic relationships among examined Albizia species and provides insights to the significance of utilizing the strengths of both molecular taxonomy and chemotaxonomy to resolve phylogenetic relationship among this genus which offers baseline for breeding programs. Future strategies to enrich taxonomic classification among Albizia includes extensive morphological characterization, DNA barcoding techniques and metabolomic profiling.

Species interactions have predictable impacts on diversification.

A fundamental goal of ecology is to reveal generalities in the myriad types of interactions among species, such as competition, mutualism and predation. Another goal is to explain the enormous differences in species richness among groups of organisms. Here, we show how these two goals are intertwined: we find that different types of species interactions have predictable impacts on rates of species diversification, which underlie richness patterns. On the basis of a systematic review, we show that interactions with positive fitness effects for individuals of a clade (e.g. insect pollination for plants) generally increase that clade's diversification rates. Conversely, we find that interactions with negative fitness effects (e.g. predation for prey, competition) generally decrease diversification rates. The sampled clades incorporate all animals and land plants, encompassing 90% of all described species across life. Overall, we show that different types of local-scale species interactions can predictably impact large-scale patterns of diversification and richness.

Comparing Rates of Linage Diversification with Rates of Size and Shape Evolution in Catarrhine Crania

Many authors have hypothesized an association between rates of morphological evolution and rates of species diversification, however, this association has yet to be empirically tested in the primate cranium. In this investigation, we used phylogeny-based approaches to examine the relationship between rates of species diversification, rates of cranial size and shape evolution, and observed cranial morphological disparity of extant catarrhines (Order: Primates). We used 34 3D landmarks digitized from 2038 crania representing 42 catarrhine species and a time-calibrated molecular phylogeny to determine the rates of evolution of cranial size and shape, rates of lineage diversification, and levels of morphological disparity by clade. The only significant relationship among these variables was for evolutionary rates of size and shape change. We discuss these results in the context of primate and mammalian macroevolution, and in light of the proposed hypothesis that size is a “line of least evolutionary resistance” in cranial evolution.