Macroevolutionary Transitions Research Articles

The influence of the land-to-sea macroevolutionary transition on vertebral column disparification in Pinnipedia.

The repeated returns of vertebrates to the marine ecosystems since the Triassic serve as an evolutionary model to understand macroevolutionary change. Here we investigate the effects of the land-to-sea transition on disparity and constraint of the vertebral column in aquatic carnivorans (Carnivora; Pinnipedia) to assess how their functional diversity and evolutionary innovations influenced major radiations of crown pinnipeds. We use three-dimensional geometric morphometrics and multivariate analysis for high-dimensional data under a phylogenetic framework to quantify vertebral size and shape in living and extinct pinnipeds. Our analysis demonstrates an important shift in vertebral column evolution by 10-12 million years ago, from an unconstrained to a constrained evolutionary scenario, a point of time that coincides with the major radiation of crown pinnipeds. Moreover, we also demonstrate that the axial skeleton of phocids and otariids followed a different path of morphological evolution that was probably driven by their specialized locomotor strategies. Despite this, we found a significant effect of habitat preference (coastal versus pelagic) on vertebral morphology of crown taxa regardless of the family they belong. In summary, our analysis provides insights into how the land-to-sea transition influenced the complex evolutionary history of pinniped vertebral morphology.

The Importance of Monitoring Non-clonal Chromosome Aberrations (NCCAs) in Cancer Research.

Cytogenetic analysis has traditionally focused on the clonal chromosome aberrations, or CCAs, and considered the large number of diverse non-clonal chromosome aberrations, or NCCAs, as insignificant noise. Our decade-long karyotype evolutionary studies have unexpectedly demonstrated otherwise. Not only the baseline of NCCAs is associated with fuzzy inheritance, but the frequencies of NCCAs can also be used to reliably measure genome or chromosome instability (CIN). According to the Genome Architecture Theory, CIN is the common driver of cancer evolution that can unify diverse molecular mechanisms, and genome chaos, including chromothripsis, chromoanagenesis, and polypoidal giant nuclear and micronuclear clusters, and various sizes of chromosome fragmentations, including extrachromosomal DNA, represent some extreme forms of NCCAs that play a key role in the macroevolutionary transition. In this chapter, the rationale, definition, brief history, and current status of NCCA research in cancer are discussed in the context of two-phased cancer evolution and karyotype-coded system information. Finally, after briefly describing various types of NCCAs, we call for more research on NCCAs in future cytogenetics.

An evolutionary history of F12 gene: Emergence, loss, and vulnerability with the environment as a driver.

In the context of macroevolutionary transitions, environmental changes prompted vertebrates already bearing genetic variations to undergo gradual adaptations resulting in profound anatomical, physiological, and behavioral adaptations. The emergence of new genes led to the genetic variation essential in metazoan evolution, just as was gene loss, both sources of genetic variation resulting in adaptive phenotypic diversity. In this context, F12-coding protein with defense and hemostatic roles emerged some 425 Mya, and it might have contributed in aquatic vertebrates to the transition from water-to-land. Conversely, the F12 loss in marine, air-breathing mammals like cetaceans has been associated with phenotypic adaptations in some terrestrial mammals in their transition to aquatic lifestyle. More recently, the advent of technological innovations in western lifestyle with blood-contacting devices and harmful environmental nanoparticles, has unfolded new roles of FXII. Environment operates as either a positive or a relaxed selective pressure on genes, and consequently genes are selected or lost. FXII, an old dog facing environmental novelties can learn new tricks and teach us new therapeutic avenues.

Evolution of nest architecture in tyrant flycatchers and allies.

Innovations in nest design are thought to be one potential factor in the evolutionary success of passerine birds (order: Passeriformes), which colonized new ecological niches as they diversified in the Oligocene and Miocene. In particular, tyrant flycatchers and their allies (parvorder: Tyrannida) are an extremely diverse group of New World suboscine passerines occupying a wide range of habitats and exhibiting substantial extant variation in nest design. To explore the evolution of nest architecture in this clade, we first described nest traits across the Tyrannida phylogeny and estimated ancestral nest conditions. We then quantified macroevolutionary transition rates between nest types, examined a potential coevolutionary relationship between nest type and habitat, and used phylogenetic mixed models to determine possible ecological and environmental correlates of nest design. The Tyrannida ancestor probably built a cup nest in a closed habitat, and dome nests independently evolved at least 15 times within this group. Both cup- and dome-nesting species diversified into semi-open and open habitats, and we did not detect a coevolutionary relationship between nest type and habitat. Furthermore, nest type was not significantly correlated with several key ecological, life-history and environmental traits, suggesting that broad variation in Tyrannida nest architecture may not easily be explained by a single factor. This article is part of the theme issue 'The evolutionary ecology of nests: a cross-taxon approach'.

Two kinds of historical explanation in Evolutionary Biology

Historical explanations in evolutionary biology are commonly characterized as narrative explanations. Examples include explanations of the evolution of particular traits and explanations of macroevolutionary transitions. In this paper I present two case studies of explanations in accounts of pathogen evolution and host-pathogen coevolution, respectively, and argue that one of them is captured well by established accounts of time-sequenced narrative explanation. The other one differs from narrative explanations in important respects, even though it shares some characteristics with them as it is also a population-level historical explanation. I thus argue that the second case represents a different kind of explanation that I call historical explanation of type phenomena. The main difference between the two kinds of explanation is the conceptualization of the explanandum phenomena as particulars or type phenomena, respectively. Narrative explanations explain particulars but also deal with generalization, regularities and type phenomena. Historical explanations of type phenomena, on the other hand, explain multiply realizable phenomena but also deal with particulars. The two kinds of explanation complement each other because they explain different aspects of evolution.

Macrostratigraphy: Insights into Cyclic and Secular Evolution of the Earth-Life System

Rocks in Earth's crust are formed, modified, and destroyed in response to myriad interactions between the solid Earth (tectonics, geodynamics), the fluid Earth (ocean-atmosphere, cryosphere), and the living Earth (evolution, biochemistry). As such, the geological record is an integrator of geological, biological, and climatological processes and their histories. Here we review contrasting perceptions of the processes that govern the formation and destruction of the geological record, beginning with the relationship between macroevolutionary patterns in the fossil and sedimentary rock records and culminating with contrasting models of rock cycling. Using the approach of macrostratigraphy, we present an integrated summary of the quantity-age properties of rocks in continental and oceanic crust. The predominant process signal in the rock quantity-age distribution in continental crust is one of episodic growth, whereas in oceanic crust it is one of continual destruction. Relatively abrupt shifts in the dominant locus of sediment deposition, from fast-cycling oceanic crust to long-term continental reservoirs, and attendant expansions and contractions in the area of crust that is emergent, are correlated in timing and magnitude with shifts in the concentration of oxygen in the atmosphere and major macroevolutionary transitions in the biosphere. The most recent of possibly two such first-ordertransitions occurred at the start of the Phanerozoic and is marked by a prominent preserved geomorphic surface known as the Great Unconformity. ▪ Macrostratigraphy uses the bulk characteristics of the rock record to probe the evolution of the Earth system. ▪ Quantifying the creation and destruction of rock units can illuminate the long-term evolution of continents and the life that inhabits them.

Comparative genomics provides insights into the aquatic adaptations of mammals

The ancestors of marine mammals once roamed the land and independently committed to an aquatic lifestyle. These macroevolutionary transitions have intrigued scientists for centuries. Here, we generated high-quality genome assemblies of 17 marine mammals (11 cetaceans and six pinnipeds), including eight assemblies at the chromosome level. Incorporating previously published data, we reconstructed the marine mammal phylogeny and population histories and identified numerous idiosyncratic and convergent genomic variations that possibly contributed to the transition from land to water in marine mammal lineages. Genes associated with the formation of blubber (NFIA), vascular development (SEMA3E), and heat production by brown adipose tissue (UCP1) had unique changes that may contribute to marine mammal thermoregulation. We also observed many lineage-specific changes in the marine mammals, including genes associated with deep diving and navigation. Our study advances understanding of the timing, pattern, and molecular changes associated with the evolution of mammalian lineages adapting to aquatic life.

\u2018Dinosaur-bird\u2019 macroevolution, locomotor modules and the origins of flight

The dinosaurian origin of birds is one of the best documented events that palaeontology has contributed to the understanding of deep time evolution. This transition has been studied on multiple fossils using numerous multidisciplinary resources, including systematics, taxonomic, anatomical, morphological, biomechanical and molecular approaches. However, whereas deep time origins and phylogenetic relationships are robust, important nuances of this transition’s dynamics remain controversial. In particular, the fossil record of several maniraptoran groups clearly shows that aerial locomotion was developed before an ‘avialization’ (i.e., before the first divergence towards avialans), thus earlier than presumed. Although aspects as important as miniaturization and the acquisition of several anatomical and morphological modifications are key factors determining such evolutionary transition, understanding this macroevolutionary trend also involves to seize the evolution of developmental systems, which requires assessing the morphological expression of integration and modularity of the locomotor apparatus throughout time. This is so because, as it happened in other flying vertebrate taxa such as pterosaurs and bats, the transformation of the maniraptoran forelimbs into flying locomotor modules must not only have involved a gradual anatomical transformation, but also a complete developmental re-patterning of the integration scheme between them and the hindlimbs. Here, we review the most relevant aspects of limb morphological transformation during the so-called ‘dinosaur-bird’ transition to stress the importance of assessing the role of modularity and morphological integration in such macroevolutionary transition, which ultimately involves the origins of flight in dinosaurs.

Molecular fossils illuminate the evolution of retroviruses following a macroevolutionary transition from land to water.

The ancestor of cetaceans underwent a macroevolutionary transition from land to water early in the Eocene Period >50 million years ago. However, little is known about how diverse retroviruses evolved during this shift from terrestrial to aquatic environments. Did retroviruses transition into water accompanying their hosts? Did retroviruses infect cetaceans through cross-species transmission after cetaceans invaded the aquatic environments? Endogenous retroviruses (ERVs) provide important molecular fossils for tracing the evolution of retroviruses during this macroevolutionary transition. Here, we use a phylogenomic approach to study the origin and evolution of ERVs in cetaceans. We identify a total of 8,724 ERVs within the genomes of 25 cetaceans, and phylogenetic analyses suggest these ERVs cluster into 315 independent lineages, each of which represents one or more independent endogenization events. We find that cetacean ERVs originated through two possible routes. 298 ERV lineages may derive from retrovirus endogenization that occurred before or during the transition from land to water of cetaceans, and most of these cetacean ERVs were reaching evolutionary dead-ends. 17 ERV lineages are likely to arise from independent retrovirus endogenization events that occurred after the split of mysticetes and odontocetes, indicating that diverse retroviruses infected cetaceans through cross-species transmission from non-cetacean mammals after the transition to aquatic life of cetaceans. Both integration time and synteny analyses support the recent or ongoing activity of multiple retroviral lineages in cetaceans, some of which proliferated into hundreds of copies within the host genomes. Although ERVs only recorded a proportion of past retroviral infections, our findings illuminate the complex evolution of retroviruses during one of the most marked macroevolutionary transitions in vertebrate history.

The Equipment of the Tyrolean Iceman: Innovation versus Adaptation in the Cultural Evolution of Prehistoric Technologies.

This study argues that the equipment of the Tyrolean Iceman offers a unique perspective for understanding the macroevolutionary-scale functional continuity between later Pleistocene and Holocene human technologies. The Iceman was discovered in 1991 in the Ötztal Alps and can be dated to around 3300 BC, corresponding to the North Italian early Copper Age. In his gear there are several technologies which are rarely found at prehistoric archaeological sites, including archery equipment, a complete set of clothing, and a personal tool kit. Our paper will discuss this technological assemblage within the framework of cultural evolutionary theories (subsequently abbreviated as CET). According to the concept of cumulative culture, tools and technologies may become the subject of cultural "descent with modification" which leads to the emergence of complex technological innovations. In conventional narratives, the Neolithic represents the single greatest macroevolutionary transition in human cultural evolution, accompanied by a whole set of novel innovations and encompassing the transition to agriculture. However, as we highlight, the Iceman's equipment includes several technologies with a pre-Neolithic cultural origin. Earlier variants of these technologies were used by cultural groups belonging to the Mesolithic and even the Upper and Middle Paleolithic. Our main goal will be to present an explanatory framework for this macroevolutionary-scale technological continuity. In order to achieve this goal, we explore the heuristic value of two basic concepts of cultural evolutionary explanations-namely, the concepts of innovation and adaptation. Building on this background, we present an overview of the data currently available on the evolutionary history of each technological adaptation found in the equipment of the Iceman. Our results suggest that these technologies were not primarily cultural innovations, but simultaneously they were "obligatory" functional adaptations with a deep evolutionary history.

Genomic and anatomical comparisons of skin support independent adaptation to life in water by cetaceans and hippos

The macroevolutionary transition from terra firma to obligatory inhabitance of the marine hydrosphere has occurred twice in the history of Mammalia: Cetacea and Sirenia. In the case of Cetacea (whales, dolphins, and porpoises), molecular phylogenies provide unambiguous evidence that fully aquatic cetaceans and semiaquatic hippopotamids (hippos) are each other's closest living relatives. Ancestral reconstructions suggest that some adaptations to the aquatic realm evolved in the common ancestor of Cetancodonta (Cetacea+ Hippopotamidae). An alternative hypothesis is that these adaptations evolved independently in cetaceans and hippos. Here, we focus on the integumentary system and evaluate these hypotheses by integrating new histological data for cetaceans and hippos, the first genome-scale data for pygmy hippopotamus, and comprehensive genomic screens and molecular evolutionary analyses for protein-coding genes that have been inactivated in hippos and cetaceans. We identified eight skin-related genes that are inactivated in both cetaceans and hippos, including genes that are related to sebaceous glands, hair follicles, and epidermal differentiation. However, none of these genes exhibit inactivating mutations that are shared by cetaceans and hippos. Mean dates for the inactivation of skin genes in these two clades serve as proxies for phenotypic changes and suggest that hair reduction/loss, the loss of sebaceous glands, and changes to the keratinization program occurred ∼16 Ma earlier in cetaceans (∼46.5 Ma) than in hippos (∼30.5 Ma). These results, together with histological differences in the integument and prior analyses of oxygen isotopes from stem hippopotamids ("anthracotheres"), support the hypothesis that aquatic skin adaptations evolved independently in hippos and cetaceans.

A farewell to arms and legs: a review of limb reduction in squamates.

Elongated snake-like bodies associated with limb reduction have evolved multiple times throughout vertebrate history. Limb-reduced squamates (lizards and snakes) account for the vast majority of these morphological transformations, and thus have great potential for revealing macroevolutionary transitions and modes of body-shape transformation. Here we present a comprehensive review on limb reduction, in which we examine and discuss research on these dramatic morphological transitions. Historically, there have been several approaches to the study of squamate limb reduction: (i) definitions of general anatomical principles of snake-like body shapes, expressed as varying relationships between body parts and morphometric measurements; (ii) framing of limb reduction from an evolutionary perspective using morphological comparisons; (iii) defining developmental mechanisms involved in the ontogeny of limb-reduced forms, and their genetic basis; (iv) reconstructions of the evolutionary history of limb-reduced lineages using phylogenetic comparative methods; (v) studies of functional and biomechanical aspects of limb-reduced body shapes; and (vi) studies of ecological and biogeographical correlates of limb reduction. For each of these approaches, we highlight their importance in advancing our understanding, as well as their weaknesses and limitations. Lastly, we provide suggestions to stimulate further studies, in which we underscore the necessity of widening the scope of analyses, and of bringing together different perspectives in order to understand better these morphological transitions and their evolution. In particular, we emphasise the importance of investigating and comparing the internal morphology of limb-reduced lizards in contrast to external morphology, which will be the first step in gaining a deeper insight into body-shape variation.

Macroevolution of Flower Color Patterning: Biased Transition Rates and Correlated Evolution with Flower Size.

Floral pigmentation patterns can both mediate plant-pollinator interactions and modify the abiotic environment of reproductive structures. To date, there have been no inquiries into the rate and directionality of macroevolutionary transitions between patterned and non-patterned petals despite their ecological importance and ubiquity across angiosperms. Petals in the Potentilleae tribe (Rosaceae) display color patterns in the ultraviolet (UV) and human-visible spectrum, or can be uniform in color (i.e., patternless). Using a phylogeny of Potentilleae, I test whether evolutionary transition rates between patterned and non-patterned petals are biased in either direction. I then examine whether UV and human-visible floral patterns are phylogenetically correlated and test the prediction that color patterns will evolve in concert with larger flowers if they function as guides to orient pollinators to floral rewards. I found that transition rates were biased toward petals that were uniform in color. Transition rates from patterned to uniformly colored petals were two and six times higher than the reverse for UV and human-visible pattern, respectively. The presence of UV and human-visible pattern evolved independently from one another. However, the evolution of human-visible pattern was associated with the evolution of larger flowers but the evolution of UV pattern was correlated with the evolution of smaller flowers. I posit that the transition bias toward non-patterned flowers may reflect developmental constraints on spatial regulation of pigments required to produce floral color patterning. The correlated evolution of larger flowers and human-visible pigmentation patterns support the hypothesis that nectar or pollen guides are more likely to evolve in larger-flowered species. This work provides insight into how transition rate bias and trait correlations can shape phylogenetic patterns of floral color pattern diversity.

Cetaceans as Exemplars of Evolution and Evolutionary Ecology: A Glossary

Extant cetaceans (whales, dolphins, and porpoises) and their extinct ancestors offer some of the strongest and best-known examples of macroevolutionary transition as well as microevolutionary adaptation. Unlike most reviews of cetacean evolution, which are intended to chronicle the timeline of cetacean ancestry, document the current knowledge of cetacean adaptations, or simply validate the brute fact of evolution, this review is instead intended to demonstrate how cetaceans fittingly illustrate hundreds of specific, detailed terms and concepts within evolutionary biology and evolutionary ecology. This review, arrayed in alphabetical glossary format, is not meant to offer an exhaustive listing of case studies or scholarly sources, but aims to show the breadth and depth of cetacean research studies supporting and investigating numerous evolutionary themes.

Adaptation to hummingbird pollination is associated with reduced diversification in Penstemon.

A striking characteristic of the Western North American flora is the repeated evolution of hummingbird pollination from insect‐pollinated ancestors. This pattern has received extensive attention as an opportunity to study repeated trait evolution as well as potential constraints on evolutionary reversibility, with little attention focused on the impact of these transitions on species diversification rates. Yet traits conferring adaptation to divergent pollinators potentially impact speciation and extinction rates, because pollinators facilitate plant reproduction and specify mating patterns between flowering plants. Here, we examine macroevolutionary processes affecting floral pollination syndrome diversity in the largest North American genus of flowering plants, Penstemon. Within Penstemon, transitions from ancestral bee‐adapted flowers to hummingbird‐adapted flowers have frequently occurred, although hummingbird‐adapted species are rare overall within the genus. We inferred macroevolutionary transition and state‐dependent diversification rates and found that transitions from ancestral bee‐adapted flowers to hummingbird‐adapted flowers are associated with reduced net diversification rate, a finding based on an estimated 17 origins of hummingbird pollination in our sample. Although this finding is congruent with hypotheses that hummingbird adaptation in North American Flora is associated with reduced species diversification rates, it contrasts with studies of neotropical plant families where hummingbird pollination has been associated with increased species diversification. We further used the estimated macroevolutionary rates to predict the expected pattern of floral diversity within Penstemon over time, assuming stable diversification and transition rates. Under these assumptions, we find that hummingbird‐adapted species are expected to remain rare due to their reduced diversification rates. In fact, current floral diversity in the sampled Penstemon lineage, where less than one‐fifth of species are hummingbird adapted, is consistent with predicted levels of diversity under stable macroevolutionary rates.

Monster or multiplacophoran: A teratological specimen of the chiton Acanthopleura granulata (Mollusca: Polyplacophora) with a valve split into independent and symmetrical halves

AbstractTeratological specimens deviate from the conserved form of their species. In doing so, they serve as natural experiments that refine our knowledge of developmental mechanisms and the natural limits of phenotypes. Here, we describe a specimen of the West Indian Fuzzy Chiton Acanthopleura granulata (Gmelin, 1791) with a fifth valve split into two halves. Using micro‐CT to non‐invasively visualize the external and internal morphology of this specimen, we find that the half valves are symmetrical and independent from each other and from any of the other valves. The presence of girdle‐like tissue between the split valves suggests that this shell abnormality arose in early development and was not the product of damage to the adult animal. While the present specimen of A. granulata is clearly abnormal for its species, its split valve may provide some insights into the developmental pathways that would underlie macroevolutionary transitions to multi‐plated chiton forms known from the fossil record.

Prenatal Development of the Humpback Whale: Growth Rate, Tooth Loss and Skull Shape Changes in an Evolutionary Framework.

Extant baleen whales (Mysticeti) share a distinct suite of extreme and unique adaptations to perform bulk filter feeding, such as a long, arched skull, and mandible and the complete loss of adult dentition in favor of baleen plates. However, mysticetes still develop tooth germs during ontogeny. In the fossil record, multiple groups document the transition from ancestral raptorial feeding to filter feeding. Fetal specimens give us an extraordinary opportunity to observe when and how this macroevolutionary transition occurs during gestation. We used iodine-enhanced and traditional CT scanning to visualize the internal anatomy of five fetuses of humpback whale representing the first two-thirds of gestation, and we combine these data with previously published reports to provide the first comprehensive qualitative description of the sequence of developmental changes that characterize the skull and dentition. We also use quantitative methods based on 3D landmarks to investigate the shape changes in the fetuses in relation to a juvenile cranial morphology. We found similarities in the ossification patterns of the humpback and other cetaceans (dolphins), but there appear to be major differences when comparing them to terrestrial artiodactyls. As for the tooth germs, this developmental sequence confirms that the tooth-to-baleen transition occurs in the last one-third of gestation. Analysis of cranial shape development revealed a progressive elongation of the rostrum and a resulting posterior movement of the nasals relative to the braincase. Future work will involve acquisition of data from other species to complete our documentation of the teeth-to-baleen transition. Anat Rec, 2018. © 2018 American Association for Anatomy.

Predator macroevolution drives trophic cascades and ecosystem functioning.

Biologists now recognize that ecology can drive evolution, and that evolution in turn produces ecological patterns. I extend this thinking to include longer time scales, suggesting that macroevolutionary transitions can create phenotypic differences among species, which then have predictable impacts on species interactions, community assembly and ecosystem functioning. Repeated speciation can exacerbate these patterns by creating communities with similar phenotypes and hence ecological impacts. Here, I use several experiments to test these ideas in dragonfly larvae that occupy ponds with fish, ponds without fish, or both. I show that macroevolutionary transitions between habitats cause fishless pond species to be more active relative to fish pond specialists, reducing prey abundance, shifting prey community composition and creating stronger trophic cascades. These effects scale up to the community level with predictable consequences for ecosystem multi-functioning. I suggest that macroevolutionary history can have predictable impacts on phenotypic traits, with consequences for interacting species and ecosystems.

How do enzymes evolve?

I will describe some insights regarding how new proteins functions evolve, via gradual, small changes in sequence. However, the mechanisms of such evolutionary micro‐transitions do not explain macro evolutionary transitions – how completely new proteins emerge, let alone how the very first enzyme(s) evolve. In the second part of my talk I will discuss our recent findings with respect to the de novo emergence of functional, globular proteins.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals.

The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent progression with a particular focus on genomic studies of marine mammals, a group of taxa that represent key macroevolutionary transitions from terrestrial to marine environments and for which available genomic resources have recently undergone notable rapid growth. Genomic studies of NMOs utilize an expanding range of approaches, including whole genome sequencing, restriction site-associated DNA sequencing, array-based sequencing of single nucleotide polymorphisms and target sequence probes (e.g., exomes), and transcriptome sequencing. These approaches generate different types and quantities of data, and many can be applied with limited or no prior genomic resources, thus overcoming one traditional limitation of research on NMOs. Within marine mammals, such studies have thus far yielded significant contributions to the fields of phylogenomics and comparative genomics, as well as enabled investigations of fitness, demography, and population structure. Here we review the primary options for generating genomic data, introduce several emerging techniques, and discuss the suitability of each approach for different applications in the study of NMOs.