Why coelacanths are not ‘living fossils’

Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage

Phylogenetic metrics are essential tools used in the study of ecology, evolution and conservation. Phylogenetic diversity (PD) in particular is one of the most prominent measures of biodiversity and is based on the idea that biological features accumulate along the edges of phylogenetic trees that are summed. We argue that PD and many other phylogenetic biodiversity metrics fail to capture an essential process that we term attrition. Attrition is the gradual loss of features through causes other than extinction. Here we introduce "EvoHeritage", a generalization of PD that is founded on the joint processes of accumulation and attrition of features. We argue that while PD measures evolutionary history, EvoHeritage is required to capture a more pertinent subset of evolutionary history including only components that have survived attrition. We show that EvoHeritage is not the same as PD on a tree with scaled edges; instead, accumulation and attrition interact in a more complex non-monophyletic way that cannot be captured by edge lengths alone. This leads us to speculate that the one-dimensional edge lengths of classic trees may be insufficiently flexible to capture the nuances of evolutionary processes. We derive a measure of EvoHeritage and show that it elegantly reproduces species richness and PD at opposite ends of a continuum based on the intensity of attrition. We demonstrate the utility of EvoHeritage in ecology as a predictor of community productivity compared with species richness and PD. We also show how EvoHeritage can quantify living fossils and resolve their associated controversy. We suggest how the existing calculus of PD-based metrics and other phylogenetic biodiversity metrics can and should be recast in terms of EvoHeritage accumulation and attrition.

Mechanisms of Rapid Karyotype Evolution in Mammals

Chromosome reshuffling events are often a foundational mechanism by which speciation can occur, giving rise to highly derivative karyotypes even amongst closely related species. Yet, the features that distinguish lineages prone to such rapid chromosome evolution from those that maintain stable karyotypes across evolutionary time are still to be defined. In this review, we summarize lineages prone to rapid karyotypic evolution in the context of Simpson's rates of evolution-tachytelic, horotelic, and bradytelic-and outline the mechanisms proposed to contribute to chromosome rearrangements, their fixation, and their potential impact on speciation events. Furthermore, we discuss relevant genomic features that underpin chromosome variation, including patterns of fusions/fissions, centromere positioning, and epigenetic marks such as DNA methylation. Finally, in the era of telomere-to-telomere genomics, we discuss the value of gapless genome resources to the future of research focused on the plasticity of highly rearranged karyotypes.

Comparative genomics of Hox and ParaHox genes among major lineages of Branchiopoda with emphasis on tadpole shrimps

Hox and ParaHox genes (HPHGs) are key developmental genes that pattern regional identity along the anterior–posterior body axis of most animals. Here, we identified HPHGs in tadpole shrimps (Pancrustacea, Branchiopoda, Notostraca), an iconic example of the so-called “living fossils” and performed a comparative genomics analysis of HPHGs and the Hox cluster among major branchiopod lineages. Notostraca possess the entire Hox complement, and the Hox cluster seems to be split into two different subclusters, although we were not able to support this finding with chromosome-level assemblies. However, the genomic structure of Hox genes in Notostraca appears more derived than that of Daphnia spp., which instead retains the plesiomorphic condition of a single compact cluster. Spinicaudata and Artemia franciscana show instead a Hox cluster subdivided across two or more genomic scaffolds with some orthologs either duplicated or missing. Yet, branchiopod HPHGs are similar among the various clades in terms of both intron length and number, as well as in their pattern of molecular evolution. Sequence substitution rates are in fact generally similar for most of the branchiopod Hox genes and the few differences we found cannot be traced back to natural selection, as they are not associated with any signals of diversifying selection or substantial switches in selective modes. Altogether, these findings do not support a significant stasis in the Notostraca Hox cluster and further confirm how morphological evolution is not tightly associated with genome dynamics.

Species delimitation and coexistence in an ancient, depauperate vertebrate clade

Background

A major challenge to understanding how biodiversity has changed over time comes from depauperons, which are long-lived lineages with presently low species diversity. The most famous of these are the coelacanths. This clade of lobe-finned fishes occupies a pivotal position on the vertebrate tree between other fishes and tetrapods. Yet only two extant species and fewer than 100 extinct forms are known from the coelacanth fossil record, which spans over 400 million years of time. Although there is evidence for the existence of additional genetically isolated extant populations, a poor understanding of morphological disparity in this clade has made quantifying coelacanth species richness difficult.

Results

Here, we quantify variation in a sample of skulls and skeletons of the Triassic eastern North American coelacanth †Diplurus that represents the largest assemblage of coelacanth individuals known. Based on the results of these quantitative comparisons, we identify a diminutive new species and show that multiple lacustrine ecosystems in the Triassic rift lakes of the Atlantic coastline harbored at least three species of coelacanths spanning two orders of magnitude in size.

Conclusions

Conceptions about the distribution of species diversity on the tree of life may be fundamentally misguided when extant diversity is used to gauge signals of extinct diversity.

Our results demonstrate how specimen-based assessments can be used to illuminate hidden biodiversity and show the utility of the fossil record for answering questions about the hidden richness of currently species-poor lineages.

Dll1 Can Function as a Ligand of Notch1 and Notch2 in the Thymic Epithelium

T-cell development in the thymus is dependent on Notch signaling induced by the interaction of Notch1, present on immigrant cells, with a Notch ligand, delta-like (Dll) 4, on the thymic epithelial cells. Phylogenetic analysis characterizing the properties of the Dll4 molecule suggests that Dll4 emerged from the common ancestor of lobe- and ray-finned fishes and diverged into bony fishes and terrestrial organisms, including mammals. The thymus evolved in cartilaginous fishes before Dll4, suggesting that T-cell development in cartilaginous fishes is dependent on Dll1 instead of Dll4. In this study, we compared the function of both Dll molecules in the thymic epithelium using Foxn1-cre and Dll4-floxed mice with conditional transgenic alleles in which the Dll1 or Dll4 gene is transcribed after the cre-mediated excision of the stop codon. The expression of Dll1 in the thymic epithelium completely restored the defect in the Dll4-deficient condition, suggesting that Dll1 can trigger Notch signaling that is indispensable for T-cell development in the thymus. Moreover, using bone marrow chimeras with Notch1- or Notch2-deficient hematopoietic cells, we showed that Dll1 is able to activate Notch signaling, which is sufficient to induce T-cell development, with both the receptors, in contrast to Dll4, which works only with Notch1, in the thymic environment. These results strongly support the hypothesis that Dll1 regulates T-cell development via Notch1 and/or Notch2 in the thymus of cartilaginous fishes and that Dll4 has replaced Dll1 in inducing thymic Notch signaling via Notch1 during evolution.

Distinguishing Evolutionary Conservation from Derivedness

While the concept of “evolutionary conservation” has enabled biologists to explain many ancestral features and traits, it has also frequently been misused to evaluate the degree of changes from a common ancestor, or “derivedness”. We propose that the distinction of these two concepts allows us to properly understand phenotypic and organismal evolution. From a methodological aspect, “conservation” mainly considers genes or traits which species have in common, while “derivedness” additionally covers those that are not commonly shared, such as novel or lost traits and genes to evaluate changes from the time of divergence from a common ancestor. Due to these differences, while conservation-oriented methods are effective in identifying ancestral features, they may be prone to underestimating the overall changes accumulated during the evolution of certain lineages. Herein, we describe our recently developed method, “transcriptomic derivedness index”, for estimating the phenotypic derivedness of embryos with a molecular approach using the whole-embryonic transcriptome as a phenotype. Although echinoderms are often considered as highly derived species, our analyses with this method showed that their embryos, at least at the transcriptomic level, may not be much more derived than those of chordates. We anticipate that the future development of derivedness-oriented methods could provide quantitative indicators for finding highly/lowly evolvable traits.

The Donnan-dominated resting state of skeletal muscle fibers contributes to resilience and longevity in dystrophic fibers

Duchenne muscular dystrophy (DMD) is an X-linked dystrophin-minus muscle-wasting disease. Ion homeostasis in skeletal muscle fibers underperforms as DMD progresses. But though DMD renders these excitable cells intolerant of exertion, sodium overloaded, depolarized, and spontaneously contractile, they can survive for several decades. We show computationally that underpinning this longevity is a strikingly frugal, robust Pump-Leak/Donnan (P-L/D) ion homeostatic process. Unlike neurons, which operate with a costly “Pump-Leak–dominated” ion homeostatic steady state, skeletal muscle fibers operate with a low-cost “Donnan-dominated” ion homeostatic steady state that combines a large chloride permeability with an exceptionally small sodium permeability. Simultaneously, this combination keeps fiber excitability low and minimizes pump expenditures. As mechanically active, long-lived multinucleate cells, skeletal muscle fibers have evolved to handle overexertion, sarcolemmal tears, ischemic bouts, etc.; the frugality of their Donnan dominated steady state lets them maintain the outsized pump reserves that make them resilient during these inevitable transient emergencies. Here, P-L/D model variants challenged with DMD-type insult/injury (low pump-strength, overstimulation, leaky Nav and cation channels) show how chronic “nonosmotic” sodium overload (observed in DMD patients) develops. Profoundly severe DMD ion homeostatic insult/injury causes spontaneous firing (and, consequently, unwanted excitation–contraction coupling) that elicits cytotoxic swelling. Therefore, boosting operational pump-strength and/or diminishing sodium and cation channel leaks should help extend DMD fiber longevity.

Comparative genomics of tadpole shrimps (Crustacea, Branchiopoda, Notostraca): Dynamic genome evolution against the backdrop of morphological stasis

This analysis presents five genome assemblies of four Notostraca taxa. Notostraca origin dates to the Permian/Upper Devonian and the extant forms show a striking morphological similarity to fossil taxa. The comparison of sequenced genomes with other Branchiopoda genomes shows that, despite the morphological stasis, Notostraca share a dynamic genome evolution with high turnover for gene families' expansion/contraction and a transposable elements content comparable to other branchiopods. While Notostraca substitutions rate appears similar or lower in comparison to other branchiopods, a subset of genes shows a faster evolutionary pace, highlighting the difficulty of generalizing about genomic stasis versus dynamism. Moreover, we found that the variation of Triops cancriformis transposable elements content appeared linked to reproductive strategies, in line with theoretical expectations. Overall, besides providing new genomic resources for the study of these organisms, which appear relevant for their ecology and evolution, we also confirmed the decoupling of morphological and molecular evolution.

A microanatomical and histological study of the scales of the Devonian sarcopterygian Miguashaia bureaui and the evolution of the squamation in coelacanths

Coelacanths have traditionally been described as morphologically conservative throughout their long evolutionary history, which spans more than 400 million years. After an initial burst during the Devonian, a morphological stasis was long thought to have prevailed since the Carboniferous, as shown by the extant Latimeria. New fossil discoveries have challenged this view, with punctual and sometimes unusual departures from the general coelacanth Bauplan. The dermal skeleton is considered to represent one, if not the main, example of morphological stasis in coelacanth evolution and as a consequence, has remained poorly surveyed. The lack of palaeohistological data on the dermoskeleton has resulted in a poor understanding of the early establishment and evolution of the coelacanth squamation. Here we describe the scales of Miguashaia bureaui from the Upper Devonian of Miguasha, Québec (Canada), revealing histological data for a Palaeozoic coelacanth in great detail and adding to our knowledge on the dermal skeleton of sarcopterygians. Miguashaia displays rounded scales ornamented by tubercules and narrow ridges made of dentine and capped with enamel. At least two generations of superimposed odontodes occur, which is reminiscent of the primitive condition of stem osteichthyans like Andreolepis or Lophosteus, and onychodonts like Selenodus. The middle vascular layer is well developed and shows traces of osteonal remodelling. The basal plate consists of a fully mineralised lamellar bone with a repetitive rotation pattern every five layers indicating a twisted plywood-like arrangement of the collagen plies. Comparisons with the extant Latimeria and other extinct taxa show that these features are consistently conserved across coelacanth evolution with only minute changes in certain taxa. The morphological and histological features displayed in the scales of Miguashaia enable us to draw a comprehensive picture of the onset of the coelacanth squamation and to propose and discuss evolutionary scenarios for the coelacanth dermoskeleton.

Bosminopsis deitersi (Crustacea: Cladocera) as an ancient species group: a revision

Water fleas (Crustacea: Cladocera) of the Family Bosminidae have been studied since the founding of paleolimnology and freshwater ecology. However, one species, Bosminopsis deitersi, stands out for its exceptional multicontinental range and broad ecological requirements. Here we use an integrated morphological and multilocus genetic approach to address the species problem in B. deitersi. We analyzed 32 populations of B. deitersi s. lat. Two nuclear and two mitochondrial loci were used to carry out the bGMYC, mPTP and STACEY algorithms for species delimitation. Detailed morphological study was also carried out across continents. The evidence indicated a widely distributed cryptic species in the Old World (Bosminopsis zernowi) that is genetically divergent from B. deitersi s.str. We revised the taxonomy and redescribed the species in this complex. Our sampling indicated that B. zernowi had weak genetic differentiation across its range. A molecular clock and biogeographic analysis with fossil calibrations suggested a Mesozoic origin for the Bosminopsis deitersi group. Our evidence rejects the single species hypothesis for B. deitersi and is consistent with an ancient species group (potentially Mesozoic) that shows marked morphological conservation. The family Bosminidae, then, has examples of both rapid morphological evolution (Holocene Bosmina), and morphological stasis (Bosminopsis).

A thirteen-million-year divergence between two lineages of Indonesian coelacanths

Coelacanth fishes of the genus Latimeria are the only surviving representatives of a basal lineage of vertebrates that originated more than 400 million years ago. Yet, much remains to be unveiled about the diversity and evolutionary history of these ‘living fossils’ using new molecular data, including the possibility of ‘cryptic’ species or unknown lineages. Here, we report the discovery of a new specimen in eastern Indonesia allegedly belonging to the species L. menadoensis. Although this specimen was found about 750 km from the known geographical distribution of the species, we found that the molecular divergence between this specimen and others of L. menadoensis was great: 1.8% compared to 0.04% among individuals of L. chalumnae, the other living species of coelacanth. Molecular dating analyses suggested a divergence date of ca. 13 million years ago between the two populations of Indonesian coelacanths. We elaborate a biogeographical scenario to explain the observed genetic divergence of Indonesian coelacanth populations based on oceanic currents and the tectonic history of the region over Miocene to recent. We hypothesize that several populations of coelacanths are likely to live further east of the present capture location, with potentially a new species that remains to be described. Based on this, we call for an international effort to take appropriate measures to protect these fascinating but vulnerable vertebrates which represent among the longest branches on the Tree of Life.

Evolution evolving? Reflections on big questions

John Bonner managed a long and productive career that balanced specialized inquiry into cellular slime molds with general investigations of big questions in evolutionary biology, such as the origins of multicellular development and the evolution of complexity. This commentary engages with his final paper ("The evolution of evolution"), which argues that the evolutionary process has changed through the history of life. In particular, Bonner emphasizes the possibility that natural selection plays different roles at different size scales. I identify some underlying assumptions in his argument and evaluate its cogency to both foster future discussion and emulate the intellectual example set by Bonner over a lifetime. This endeavor is important beyond Bonner's own theoretical disposition because similar issues are visible in controversies about the possibility of an extended evolutionary synthesis.

Development and growth of the pectoral girdle and fin skeleton in the extant coelacanth Latimeria chalumnae

The monobasal pectoral fins of living coelacanths and lungfishes are homologous to the forelimbs of tetrapods and are thus critical to investigate the origin thereof. However, it remains unclear whether the similarity in the asymmetrical endoskeletal arrangement of the pectoral fins of coelacanths reflects the evolution of the pectoral appendages in sarcopterygians. Here, we describe for the first time the development of the pectoral fin and shoulder girdle in the extant coelacanth Latimeria chalumnae, based on the tomographic acquisition of a growth series. The pectoral girdle and pectoral fin endoskeleton are formed early in development with a radially outward growth of the endoskeletal elements. The visualization of the pectoral girdle during development shows a reorientation of the girdle between the fetus and pup 1 stages, creating a contact between the scapulocoracoids and the clavicles in the ventro-medial region. Moreover, we observed a splitting of the pre- and post-axial cartilaginous plates in respectively pre-axial radials and accessory elements on one hand, and in post-axial accessory elements on the other hand. However, the mechanisms involved in the splitting of the cartilaginous plates appear different from those involved in the formation of radials in actinopterygians. Our results show a proportional reduction of the proximal pre-axial radial of the fin, rendering the external morphology of the fin more lobe-shaped, and a spatial reorganization of elements resulting from the fragmentation of the two cartilaginous plates. Latimeria development hence supports previous interpretations of the asymmetrical pectoral fin skeleton as being plesiomorphic for coelacanths and sarcopterygians.

Variation across Species and Levels: Implications for Model Species Research

The selection of model species tends to involve two typically unstated assumptions, namely: (1) that the similarity between species decreases steadily with phylogenetic distance, and (2) that similarities are greater at lower levels of biological organization. The first assumption holds on average, but species similarities tend to decrease with the square root of divergence time, rather than linearly, and lineages with short generation times (which includes most model species) tend to diverge faster than average, making the decrease in similarity non-monotonic. The second assumption is more difficult to test. Comparative molecular research has traditionally emphasized species similarities over differences, whereas comparative research at higher levels of organization frequently highlights the species differences. However, advances in comparative genomics have brought to light a great variety of species differences, not just in gene regulation but also in protein coding genes. Particularly relevant are cases in which homologous high-level characters are based on non-homologous genes. This phenomenon of non-orthologous gene displacement, or "deep non-homology," indicates that species differences at the molecular level can be surprisingly large. Given these observations, it is not surprising that some findings obtained in model species do not generalize across species as well as researchers had hoped, even if the research is molecular.

Re-thinking the social ladder approach for elucidating the evolution and molecular basis of insect societies

The evolution of large insect societies is a major evolutionary transition that occurred in the long-extinct ancestors of termites, ants, corbiculate bees, and vespid wasps. Researchers have long used 'social ladder thinking': assuming progressive stepwise phenotypic evolution and asserting that extant species with simple societies (e.g. some halictid bees) represent the ancestors of species with complex societies, and thus provide insight into general early steps of eusocial evolution. We discuss how this is inconsistent with data and modern evolutionary 'tree thinking'. Phylogenetic comparative methods with broad sampling provide the best means to make rigorous inferences about ancestral traits and evolutionary transitions that occurred within each lineage, and to determine whether consistent phenotypic and genomic changes occurred across independent lineages.

Rethinking Living Fossils

Biologists would be mistaken if they relegated living fossils to paleontological inquiry or assumed that the concept is dead. It is now used to describe entities ranging from viruses to higher taxa, despite recent warnings of misleading inferences. Current work on character evolution illustrates how analyzing living fossils and stasis in terms of parts (characters) and wholes (e.g., organisms and lineages) advances our understanding of prolonged stasis at many hierarchical levels. Instead of viewing the concept's task as categorizing living fossils, we show how its primary role is to mark out what is in need of explanation, accounting for the persistence of both molecular and morphological traits. Rethinking different conceptions of living fossils as specific hypotheses reveals novel avenues for research that integrate phylogenetics, ecological and evolutionary modeling, and evo-devo to produce a more unified theoretical outlook.

Phylogeography of Arenaria balearica L. (Caryophyllaceae): evolutionary history of a disjunct endemic from the Western Mediterranean continental islands

Although it has been traditionally accepted that Arenaria balearica (Caryophyllaceae) could be a relict Tertiary plant species, this has never been experimentally tested. Nor have the palaeohistorical reasons underlying the highly fragmented distribution of the species in the Western Mediterranean region been investigated. We have analysed AFLP data (213) and plastid DNA sequences (226) from a total of 250 plants from 29 populations sampled throughout the entire distribution range of the species in Majorca, Corsica, Sardinia, and the Tuscan Archipelago. The AFLP data analyses indicate very low geographic structure and population differentiation. Based on plastid DNA data, six alternative phylogeographic hypotheses were tested using Approximate Bayesian Computation (ABC). These analyses revealed ancient area fragmentation as the most probable scenario, which is in accordance with the star-like topology of the parsimony network that suggests a pattern of long term survival and subsequent in situ differentiation. Overall low levels of genetic diversity and plastid DNA variation were found, reflecting evolutionary stasis of a species preserved in locally long-term stable habitats.

Incorporating tree-thinking and evolutionary time scale into developmental biology

Phylogenetic approaches are indispensable in any comparative molecular study involving multiple species. These approaches are in increasing demand as the amount and availability of DNA sequence information continues to increase exponentially, even for organisms that were previously not extensively studied. Without the sound application of phylogenetic concepts and knowledge, one can be misled when attempting to infer ancestral character states as well as the timing and order of evolutionary events, both of which are frequently exerted in evolutionary developmental biology. The ignorance of phylogenetic approaches can also impact non-evolutionary studies and cause misidentification of the target gene or protein to be examined in functional characterization. This review aims to promote tree-thinking in evolutionary conjecture and stress the importance of a sense of time scale in cross-species comparisons, in order to enhance the understanding of phylogenetics in all biological fields including developmental biology. To this end, molecular phylogenies of several developmental regulatory genes, including those denoted as "cryptic pan-vertebrate genes", are introduced as examples.

Ancestor-descendant relationships in evolution: origin of the extant pygmy right whale, Caperea marginata

Ancestor-descendant relationships (ADRs), involving descent with modification, are the fundamental concept in evolution, but are usually difficult to recognize. We examined the cladistic relationship between the only reported fossil pygmy right whale, †Miocaperea pulchra, and its sole living relative, the enigmatic pygmy right whale Caperea marginata, the latter represented by both adult and juvenile specimens. †Miocaperea is phylogenetically bracketed between juvenile and adult Caperea marginata in morphologically based analyses, thus suggesting a possible ADR-the first so far identified within baleen whales (Cetacea: Mysticeti). The †Miocaperea-Caperea lineage may show long-term morphological stasis and, in turn, punctuated equilibrium.

The coelacanth: Can a "living fossil" have active transposable elements in its genome?

The coelacanth has long been regarded as a "living fossil," with extant specimens looking very similar to fossils dating back to the Cretaceous period. The hypothesis of a slowly or even not evolving genome has been proposed to account for this apparent morphological stasis. While this assumption seems to be sustained by different evolutionary analyses on protein-coding genes, recent studies on transposable elements have provided more conflicting results. Indeed, the coelacanth genome contains many transposable elements and has been shaped by several major bursts of transposition during evolution. In addition, comparison of orthologous genomic regions from the genomes of the 2 extant coelacanth species L. chalumnae and L. menadoensis revealed multiple species-specific insertions, indicating transposable element recent activity and contribution to post-speciation genome divergence. These observations, which do not support the genome stasis hypothesis, challenge either the impact of transposable elements on organismal evolution or the status of the coelacanth as a "living fossil." Closer inspection of fossil and molecular data indicate that, even if coelacanths might evolve more slowly than some other lineages due to demographic and/or ecological factors, this variation is still in the range of a "non-fossil" vertebrate species.

The coelacanth rostral organ is a unique low-resolution electro-detector that facilitates the feeding strike

The cartilaginous and non-neopterygian bony fishes have an electric sense typically comprised of hundreds or thousands of sensory canals distributed in broad clusters over the head. This morphology facilitates neural encoding of local electric field intensity, orientation, and polarity, used for determining the position of nearby prey. The coelacanth rostral organ electric sense, however, is unique in having only three paired sensory canals with distribution restricted to the dorsal snout, raising questions about its function. To address this, we employed magnetic resonance imaging methods to map electrosensory canal morphology in the extant coelacanth, Latimeria chalumnae, and a simple dipole 'rabbit ears' antennae model with toroidal gain function to approximate their directional sensitivity. This identified a unique focal region of electrosensitivity directly in front of the mouth, and is the first evidence of a low-resolution electro-detector that solely facilitates prey ingestion.

Interspecies insertion polymorphism analysis reveals recent activity of transposable elements in extant coelacanths

Coelacanths are lobe-finned fish represented by two extant species, Latimeria chalumnae in South Africa and Comoros and L. menadoensis in Indonesia. Due to their intermediate phylogenetic position between ray-finned fish and tetrapods in the vertebrate lineage, they are of great interest from an evolutionary point of view. In addition, extant specimens look similar to 300 million-year-old fossils; because of their apparent slowly evolving morphology, coelacanths have been often described as « living fossils ». As an underlying cause of such a morphological stasis, several authors have proposed a slow evolution of the coelacanth genome. Accordingly, sequencing of the L. chalumnae genome has revealed a globally low substitution rate for protein-coding regions compared to other vertebrates. However, genome and gene evolution can also be influenced by transposable elements, which form a major and dynamic part of vertebrate genomes through their ability to move, duplicate and recombine. In this work, we have searched for evidence of transposition activity in coelacanth genomes through the comparative analysis of orthologous genomic regions from both Latimeria species. Comparison of 5.7 Mb (0.2%) of the L. chalumnae genome with orthologous Bacterial Artificial Chromosome clones from L. menadoensis allowed the identification of 27 species-specific transposable element insertions, with a strong relative contribution of CR1 non-LTR retrotransposons. Species-specific homologous recombination between the long terminal repeats of a new coelacanth endogenous retrovirus was also detected. Our analysis suggests that transposon activity is responsible for at least 0.6% of genome divergence between both Latimeria species. Taken together, this study demonstrates that coelacanth genomes are not evolutionary inert: they contain recently active transposable elements, which have significantly contributed to post-speciation genome divergence in Latimeria.

Permian-Triassic Osteichthyes (bony fishes): diversity dynamics and body size evolution

The Permian and Triassic were key time intervals in the history of life on Earth. Both periods are marked by a series of biotic crises including the most catastrophic of such events, the end-Permian mass extinction, which eventually led to a major turnover from typical Palaeozoic faunas and floras to those that are emblematic for the Mesozoic and Cenozoic. Here we review patterns in Permian-Triassic bony fishes, a group whose evolutionary dynamics are understudied. Based on data from primary literature, we analyse changes in their taxonomic diversity and body size (as a proxy for trophic position) and explore their response to Permian-Triassic events. Diversity and body size are investigated separately for different groups of Osteichthyes (Dipnoi, Actinistia, 'Palaeopterygii', 'Subholostei', Holostei, Teleosteomorpha), within the marine and freshwater realms and on a global scale (total diversity) as well as across palaeolatitudinal belts. Diversity is also measured for different palaeogeographical provinces. Our results suggest a general trend from low osteichthyan diversity in the Permian to higher levels in the Triassic. Diversity dynamics in the Permian are marked by a decline in freshwater taxa during the Cisuralian. An extinction event during the end-Guadalupian crisis is not evident from our data, but 'palaeopterygians' experienced a significant body size increase across the Guadalupian-Lopingian boundary and these fishes upheld their position as large, top predators from the Late Permian to the Late Triassic. Elevated turnover rates are documented at the Permian-Triassic boundary, and two distinct diversification events are noted in the wake of this biotic crisis, a first one during the Early Triassic (dipnoans, actinistians, 'palaeopterygians', 'subholosteans') and a second one during the Middle Triassic ('subholosteans', neopterygians). The origination of new, small taxa predominantly among these groups during the Middle Triassic event caused a significant reduction in osteichthyan body size. Neopterygii, the clade that encompasses the vast majority of extant fishes, underwent another diversification phase in the Late Triassic. The Triassic radiation of Osteichthyes, predominantly of Actinopterygii, which only occurred after severe extinctions among Chondrichthyes during the Middle-Late Permian, resulted in a profound change within global fish communities, from chondrichthyan-rich faunas of the Permo-Carboniferous to typical Mesozoic and Cenozoic associations dominated by actinopterygians. This turnover was not sudden but followed a stepwise pattern, with leaps during extinction events.

Relict species: a relict concept?

Relict species have always beguiled evolutionary biologists and biogeographers, who often view them as fascinating 'living fossils' or remnants of old times. Consequently, they are believed to provide interesting and important information on a vanished past and are used to understand the evolution of clades and biotas. The information that relicts provide can, however, be misleading and overemphasised when it is not remembered that they belong to groups or biotas that are mostly extinct. For example, relict species imply regional extinctions and, for this reason, they cannot simultaneously provide evidence of local biota permanence. Here we consider carefully misconceptions about relict species and highlight more clearly their evolutionary and biogeographical significance.

Model organisms in evo-devo: promises and pitfalls of the comparative approach

Evolutionary developmental biology (evo-devo) is a rapidly growing discipline whose ambition is to address questions that are of relevance to both evolutionary biology and developmental biology. This field has been increasingly progressing as a new and independent comparative science. However, we argue that evo-devo's comparative approach is challenged by several metaphysical, methodological and socio-disciplinary issues related to the foundation of heuristic functions of model organisms and the possible criteria to be adopted for their selection. In addition, new tools have to be developed to deal with newly chosen model organisms. Therefore, we present a modelling framework suitable to integrate data on individual variation into evo-devo studies on new model organisms and thus to compensate for current idealization practices deliberately suppressing variation.

Is evolutionary biology becoming too politically correct? A reflection on the scala naturae, phylogenetically basal clades, anatomically plesiomorphic taxa, and 'lower' animals

The notion of scala naturae dates back to thinkers such as Aristotle, who placed plants below animals and ranked the latter along a graded scale of complexity from 'lower' to 'higher' animals, such as humans. In the last decades, evolutionary biologists have tended to move from one extreme (i.e. the idea of scala naturae or the existence of a general evolutionary trend in complexity from 'lower' to "higher" taxa, with Homo sapiens as the end stage) to the other, opposite, extreme (i.e. to avoid using terms such as 'phylogenetically basal' and 'anatomically plesiomorphic' taxa, which are seen as the undesired vestige of old teleological theories). The latter view tries to avoid any possible connotations with the original anthropocentric idea of a scala naturae crowned by man and, in that sense, it can be regarded as a more politically correct view. In the past years and months there has been renewed interest in these topics, which have been discussed in various papers and monographs that tend to subscribe, in general, to the points defended in the more politically correct view. Importantly, most evolutionary and phylogenetic studies of tetrapods and other vertebrates, and therefore most discussions on the scala naturae and related issues have been based on hard tissue and, more recently, on molecular data. Here we provide the first discussion of these topics based on a comparative myological study of all the major vertebrate clades and of myological cladistic and Bayesian phylogenetic analyses of bony fish and tetrapods, including Primates. We specifically (i) contradict the notions of a scala naturae or evolutionary progressive trends leading to more complexity in 'higher' animals and culminating in Homo sapiens, and (ii) stress that the refutation of these old notions does not necessarily mean that one should not keep using the terms 'phylogenetically basal' and particularly 'anatomically plesiomorphic' to refer to groups such as the urodeles within the Tetrapoda, or the strepsirrhines and lemurs within the Primates, for instance. This review will contribute to improving our understanding of these broad evolutionary issues and of the evolution of the vertebrate Bauplans, and hopefully will stimulate future phylogenetic, evolutionary and developmental studies of these clades.

A tetrapod-like repertoire of innate immune receptors and effectors for coelacanths

The recent availability of both robust transcriptome and genome resources for coelacanth (Latimeria chalumnae) has led to unique discoveries for coelacanth immunity such as the lack of IgM, a central component of adaptive immunity. This study was designed to more precisely address the origins and evolution of gene families involved in the initial recognition and response to microbial pathogens, which effect innate immunity. Several multigene families involved in innate immunity are addressed, including: Toll-like receptors (TLRs), retinoic acid inducible gene 1 (RIG1)-like receptors (RLRs), the nucleotide-binding domain and leucine-rich repeat containing proteins (NLRs), diverse immunoglobulin domain-containing proteins (DICP) and modular domain immune-type receptors (MDIRs). Our analyses also include the tripartite motif-containing proteins (TRIM), which are involved in pathogen recognition as well as the positive regulation of antiviral immunity. Finally, this study addressed some of the downstream effectors of the antimicrobial response including IL-1 family members, type I and II interferons (IFN) and IFN-stimulated effectors (ISGs). Collectively, the genes and gene families in coelacanth that effect innate immune functions share characteristics both in content, structure and arrangement with those found in tetrapods but not in teleosts. The findings support the sister group relationship of coelacanth fish with tetrapods.

Boom and bust: ancient and recent diversification in bichirs (Polypteridae: Actinopterygii), a relictual lineage of ray-finned fishes

Understanding the history that underlies patterns of species richness across the Tree of Life requires an investigation of the mechanisms that not only generate young species-rich clades, but also those that maintain species-poor lineages over long stretches of evolutionary time. However, diversification dynamics that underlie ancient species-poor lineages are often hidden due to a lack of fossil evidence. Using information from the fossil record and time calibrated molecular phylogenies, we investigate the history of lineage diversification in Polypteridae, which is the sister lineage of all other ray-finned fishes (Actinopterygii). Despite originating at least 390 million years (Myr) ago, molecular timetrees support a Neogene origin for the living polypterid species. Our analyses demonstrate polypterids are exceptionally species depauperate with a stem lineage duration that exceeds 380 million years (Ma) and is significantly longer than the stem lineage durations observed in other ray-finned fish lineages. Analyses of the fossil record show an early Late Cretaceous (100.5-83.6 Ma) peak in polypterid genus richness, followed by 60 Ma of low richness. The Neogene species radiation and evidence for high-diversity intervals in the geological past suggest a "boom and bust" pattern of diversification that contrasts with common perceptions of relative evolutionary stasis in so-called "living fossils."

Transcriptional activity of transposable elements in coelacanth

The morphological stasis of coelacanths has long suggested a slow evolutionary rate. General genomic stasis might also imply a decrease of transposable elements activity. To evaluate the potential activity of transposable elements (TEs) in "living fossil" species, transcriptomic data of Latimeria chalumnae and its Indonesian congener Latimeria menadoensis were compared through the RNA-sequencing mapping procedures in three different organs (liver, testis, and muscle). The analysis of coelacanth transcriptomes highlights a significant percentage of transcribed TEs in both species. Major contributors are LINE retrotransposons, especially from the CR1 family. Furthermore, some particular elements such as a LF-SINE and a LINE2 sequences seem to be more expressed than other elements. The amount of TEs expressed in testis suggests possible transposition burst in incoming generations. Moreover, significant amount of TEs in liver and muscle transcriptomes were also observed. Analyses of elements displaying marked organ-specific expression gave us the opportunity to highlight exaptation cases, that is, the recruitment of TEs as new cellular genes, but also to identify a new Latimeria-specific family of Short Interspersed Nuclear Elements called CoeG-SINEs. Overall, transcriptome results do not seem to be in line with a slow-evolving genome with poor TE activity.

Revealing less derived nature of cartilaginous fish genomes with their evolutionary time scale inferred with nuclear genes

Cartilaginous fishes, divided into Holocephali (chimaeras) and Elasmoblanchii (sharks, rays and skates), occupy a key phylogenetic position among extant vertebrates in reconstructing their evolutionary processes. Their accurate evolutionary time scale is indispensable for better understanding of the relationship between phenotypic and molecular evolution of cartilaginous fishes. However, our current knowledge on the time scale of cartilaginous fish evolution largely relies on estimates using mitochondrial DNA sequences. In this study, making the best use of the still partial, but large-scale sequencing data of cartilaginous fish species, we estimate the divergence times between the major cartilaginous fish lineages employing nuclear genes. By rigorous orthology assessment based on available genomic and transcriptomic sequence resources for cartilaginous fishes, we selected 20 protein-coding genes in the nuclear genome, spanning 2973 amino acid residues. Our analysis based on the Bayesian inference resulted in the mean divergence time of 421 Ma, the late Silurian, for the Holocephali-Elasmobranchii split, and 306 Ma, the late Carboniferous, for the split between sharks and rays/skates. By applying these results and other documented divergence times, we measured the relative evolutionary rate of the Hox A cluster sequences in the cartilaginous fish lineages, which resulted in a lower substitution rate with a factor of at least 2.4 in comparison to tetrapod lineages. The obtained time scale enables mapping phenotypic and molecular changes in a quantitative framework. It is of great interest to corroborate the less derived nature of cartilaginous fish at the molecular level as a genome-wide phenomenon.

Multiple global radiations in tadpole shrimps challenge the concept of 'living fossils'

'Living fossils', a phrase first coined by Darwin, are defined as species with limited recent diversification and high morphological stasis over long periods of evolutionary time. Morphological stasis, however, can potentially lead to diversification rates being underestimated. Notostraca, or tadpole shrimps, is an ancient, globally distributed order of branchiopod crustaceans regarded as 'living fossils' because their rich fossil record dates back to the early Devonian and their morphology is highly conserved. Recent phylogenetic reconstructions have shown a strong biogeographic signal, suggesting diversification due to continental breakup, and widespread cryptic speciation. However, morphological conservatism makes it difficult to place fossil taxa in a phylogenetic context. Here we reveal for the first time the timing and tempo of tadpole shrimp diversification by inferring a robust multilocus phylogeny of Branchiopoda and applying Bayesian divergence dating techniques using reliable fossil calibrations external to Notostraca. Our results suggest at least two bouts of global radiation in Notostraca, one of them recent, so questioning the validity of the 'living fossils' concept in groups where cryptic speciation is widespread.