Vertebrate History Research Articles

How compactness affects long bone resistance to compression-An investigation into the rhinoceros humerus.

The functional signal of bone internal structure has been widely studied. Isolated form-function relationships have often been assumed from the observation of presumed morphofunctional relationships, but have never been truly tested. Indeed, distinct bone microanatomical feature co-evolve in response to various constraints that are difficult to detangle. This study tested for the first time the impact of various microanatomical parameters taken one by one, plus some in pairs, on bone strength under compression using biomechanical modelling. We carried out finite element analyses on humerus models, obtained from a white rhinoceros, with different heterogeneous internal structures, and analysed the magnitude and distribution of von Mises stresses. These tests validated earlier hypotheses of form-function relationships about the greater resistance to compression provided by the thickening of the cortex and the filling of the medullary area by trabecular bone and highlighted the stronger impact of increasing trabecular bone compactness than of avoiding an open medullary cavity. By making it possible to estimate the relative impact of each parameter and ofcombinations of microanatomical features, they also showed the more limited impact of the trabecular bone compactness in the epiphyses to resist compression, and the fact that microanatomical changes of opposite but of similar amplitude impact can compensate each other, but that the impact of the sum of two negative microanatomical changes far exceeds the sum of the impacts of each of the two changes taken separately. These results contribute to a better understanding of bone adaptation and form-function relationships so that they later can be used with confidence for palaeobiological inferences on fossil specimens, contributing to a better understanding of skeletal evolution during the evolutionary history of vertebrates. They also highlight the potential of taking internal structure into account in the bone biomechanical analyses. In addition, they can be used in bioinspiration to design resistant structures subjected to compression.

Comparative genomics illuminates karyotype and sex chromosome evolution of sharks

Chondrichthyes is an important lineage to reconstruct the evolutionary history of vertebrates. Here, we analyzed genome synteny for six chondrichthyan chromosome-level genomes. Our comparative analysis reveals a slow evolutionary rate of chromosomal changes, with infrequent but independent fusions observed in sharks, skates, and chimaeras. The chondrichthyan common ancestor had a proto-vertebrate-like karyotype, including the presence of 18 microchromosome pairs. The X chromosome is a conversed microchromosome shared by all sharks, suggesting a likely common origin of the sex chromosome at least 181 million years ago. We characterized the Y chromosomes of two sharks that are highly differentiated from the X except for a small young evolutionary stratum and a small pseudoautosomal region. We found that shark sex chromosomes lack global dosage compensation but that dosage-sensitive genes are locally compensated. Our study on shark chromosome evolution enhances our understanding of shark sex chromosomes and vertebrate chromosome evolution.

Regulation mechanism of endochondral ossification in Rana zhenhaiensis during metamorphosis based on histomorphology and transcriptome analyses

Endochondral ossification plays a crucial role in the limb development of amphibians. This study explored the ossification sequence in the hindlimb of Rana zhenhaiensis tadpoles and the correlation between thyroid hormones (THs) and endochondral ossification via histomorphology and transcriptional analyses. Our results suggest that ossification of the femur and tibiofibula was initiated during the period of high THs activity (metamorphosis climax). In addition, the results of differentially expressed gene analyses in the hindlimb and tail showed that systemic factors, transcription factors, and locally secreted factors interacted with each other during the metamorphosis climax to regulate the occurrence of endochondral ossification. These results will enrich the morphological data of anurans and provide scientific reference for the evolutionary history of vertebrates.

Comparing cranial biomechanics between Barbourofelis fricki and Smilodon fatalis: Is there a universal killing-bite among saber-toothed predators?

Saber-tooths, extinct apex predators with long and blade-like upper canines, have appeared iteratively at least five times in the evolutionary history of vertebrates. Although saber-tooths exhibit a relatively diverse range of morphologies, it is widely accepted that all killed their prey using the same predatory behavior. In this study, we CT-scanned the skull of Barbourofelis fricki and compared its cranial mechanics using finite element analysis (FEA) with that of Smilodon fatalis. Our aim was to investigate potential variations in killing behavior between two dirk-toothed sabretooths from the Miocene and Pleistocene of North America. The study revealed that B. fricki had a stoutly-built skull capable of withstanding stress in various prey-killing scenarios, while the skull of S. fatalis appeared less optimized for supporting stress, which highlights the highly derived saber-tooth morphology of the former. The results may indicate that B. fricki was more of a generalist in prey-killing compared to S. fatalis, which experiences lower stresses under stabbing loads. We hypothesize that morphological specialization in saber-tooths does not necessarily indicate ecological specialization. Our results support the notion that morphological convergence among saber-toothed cats may obscure differences in hunting strategies employed to dispatch their prey. Our findings challenge the assumption of the universally assumed canine-shear biting as the prey-killing behavior of all saber-toothed cats. However, further research involving a wider range of dirk and scimitar-toothed forms could provide additional insights into the diversity of cranial biomechanics within this fascinating group of extinct mammalian predators.

Evolutionary analysis of SLC10 family members and insights into function and expression regulation of lamprey NTCP.

The Na ( +)-taurocholate cotransporting polypeptide (NTCP) is a member of the solute carrier family 10 (SLC10), which consists of 7 members (SLC10a1-SLC10a7). NTCP is a transporter localized to the basolateral membrane of hepatocytes and is primarily responsible for the absorption of bile acids. Although mammalian NTCP has been extensively studied, little is known about the lamprey NTCP (L-NTCP). Here we show that L-NTCP follows the biological evolutionary history of vertebrates, with conserved domain, motif, and similar tertiary structure to higher vertebrates. L-NTCP is localized to the cell surface of lamprey primary hepatocytes by immunofluorescence analysis. HepG2 cells overexpressing L-NTCP also showed the distribution of L-NTCP on the cell surface. The expression profile of L-NTCP showed that the expression of NTCP is highest in lamprey liver tissue. L-NTCP also has the ability to transport bile acids, consistent with its higher vertebrate orthologs. Finally, using a farnesoid X receptor (FXR) antagonist, RT-qPCR and flow cytometry results showed that L-NTCP is negatively regulated by the nuclear receptor FXR. This study is important for understanding the adaptive mechanisms of bile acid metabolism after lamprey biliary atresia based on understanding the origin, evolution, expression profile, biological function, and expression regulation of L-NTCP.

Quantitative functional imaging of the pigeon brain: implications for the evolution of avian powered flight.

The evolution of flight is a rare event in vertebrate history, and one that demands functional integration across multiple anatomical/physiological systems. The neuroanatomical basis for such integration and the role that brain evolution assumes in behavioural transformations remain poorly understood. We make progress by (i) generating a positron emission tomography (PET)-based map of brain activity for pigeons during rest and flight, (ii) using these maps in a functional analysis of the brain during flight, and (iii) interpreting these data within a macroevolutionary context shaped by non-avian dinosaurs. Although neural activity is generally conserved from rest to flight, we found significant increases in the cerebellum as a whole and optic flow pathways. Conserved activity suggests processing of self-movement and image stabilization are critical when a bird takes to the air, while increased visual and cerebellar activity reflects the importance of integrating multimodal sensory information for flight-related movements. A derived cerebellar capability likely arose at the base of maniraptoran dinosaurs, where volumetric expansion and possible folding directly preceded paravian flight. These data represent an important step toward establishing how the brain of modern birds supports their unique behavioural repertoire and provide novel insights into the neurobiology of the bird-like dinosaurs that first achieved powered flight.

The hagfish genome and the evolution of vertebrates

As the only surviving lineages of jawless fishes, hagfishes and lampreys provide a crucial window into early vertebrate evolution1–3. Here we investigate the complex history, timing and functional role of genome-wide duplications4–7 and programmed DNA elimination8,9 in vertebrates in the light of a chromosome-scale genome sequence for the brown hagfish Eptatretus atami. Combining evidence from syntenic and phylogenetic analyses, we establish a comprehensive picture of vertebrate genome evolution, including an auto-tetraploidization (1RV) that predates the early Cambrian cyclostome–gnathostome split, followed by a mid–late Cambrian allo-tetraploidization (2RJV) in gnathostomes and a prolonged Cambrian–Ordovician hexaploidization (2RCY) in cyclostomes. Subsequently, hagfishes underwent extensive genomic changes, with chromosomal fusions accompanied by the loss of genes that are essential for organ systems (for example, genes involved in the development of eyes and in the proliferation of osteoclasts); these changes account, in part, for the simplification of the hagfish body plan1,2. Finally, we characterize programmed DNA elimination in hagfish, identifying protein-coding genes and repetitive elements that are deleted from somatic cell lineages during early development. The elimination of these germline-specific genes provides a mechanism for resolving genetic conflict between soma and germline by repressing germline and pluripotency functions, paralleling findings in lampreys10,11. Reconstruction of the early genomic history of vertebrates provides a framework for further investigations of the evolution of cyclostomes and jawed vertebrates.

Dumbbell-shaped brains of Polish crested chickens as a model system for the evolution of novel brain morphologies.

The evolutionary history of vertebrates is replete with emergence of novel brain morphologies, including the origin of the human brain. Existing model organisms and toolkits for investigating drivers of neuroanatomical innovations have largely proceeded on mammals. As such, a compelling non-mammalian model system would facilitate our understanding of how unique brain morphologies evolve across vertebrates. Here, we present the domestic chicken breed, white crested Polish chickens, as an avian model for investigating how novel brain morphologies originate. Most notably, these crested chickens exhibit cerebral herniation from anterodorsal displacement of the telencephalon, which results in a prominent protuberance on the dorsal aspect of the skull. We use a high-density geometric morphometric approach on cephalic endocasts to characterize their brain morphology. Compared with standard white Leghorn chickens (WLCs) and modern avian diversity, the results demonstrate that crested chickens possess a highly variable and unique overall brain configuration. Proportional sizes of neuroanatomical regions are within the observed range of extant birds sampled in this study, but Polish chickens differ from WLCs in possessing a relatively larger cerebrum and smaller cerebellum and medulla. Given their accessibility, phylogenetic proximity, and unique neuroanatomy, we propose that crested breeds, combined with standard chickens, form a promising comparative system for investigating the emergence of novel brain morphologies.

Lasanius, an exceptionally preserved Silurian jawless fish from Scotland

AbstractThe fossil record of non‐biomineralizing, soft‐bodied taxa is our only direct evidence of the early history of vertebrates. A robust reconstruction of the affinities of these taxa is critical to unlocking vertebrate origins and understanding the evolution of skeletal tissues, but these taxa invariably have unstable and poorly supported phylogenetic positions. At the cusp between mineralized bony vertebrates and entirely soft‐bodied vertebrates is the enigmaticLasanius, a purported anaspid from the Silurian of Scotland. Interpretations of its affinity and significance are conflicted, principally because of its poorly understood anatomy due to taphonomic distortion and loss of soft‐tissues. Here we use an array of modern techniques to reassess the anatomy ofLasaniusvia a comprehensive study of 229 complete and partial specimens. A new reconstruction clarifies the identity and position of preserved features, including paired sensory organs, a notochord, and digestive tract, supporting the vertebrate affinities of this genus. SEM‐EDS trace element mapping suggests a bone‐like composition of mineralized parts, but finds no evidence for mineralized dermal armour. Phylogenetic analysis recoversLasaniusas an early stem‐cyclostome, and subsequent analysis supports the rejection of alternative placements (such as stem‐gnathostome). We highlight that while distinguishing between the early cyclostome and gnathostome condition is problematic, increasing confidence in the anatomy of key taxa, such asLasanius, is vital for increased stability throughout the early vertebrate tree.

Amblyopinae Mitogenomes Provide Novel Insights into the Paraphyletic Origin of Their Adaptation to Mudflat Habitats.

The water-to-land transition is one of the most important events in evolutionary history of vertebrates. However, the genetic basis underlying many of the adaptations during this transition remains unclear. Mud-dwelling gobies in the subfamily Amblyopinae are one of the teleosts lineages that show terrestriality and provide a useful system for clarifying the genetic changes underlying adaptations to terrestrial life. Here, we sequenced the mitogenome of six species in the subfamily Amblyopinae. Our results revealed a paraphyletic origin of Amblyopinae with respect to Oxudercinae, which are the most terrestrial fishes and lead an amphibious life in mudflats. This partly explains the terrestriality of Amblyopinae. We also detected unique tandemly repeated sequences in the mitochondrial control region in Amblyopinae, as well as in Oxudercinae, which mitigate oxidative DNA damage stemming from terrestrial environmental stress. Several genes, such as ND2, ND4, ND6 and COIII, have experienced positive selection, suggesting their important roles in enhancing the efficiency of ATP production to cope with the increased energy requirements for life in terrestrial environments. These results strongly suggest that the adaptive evolution of mitochondrial genes has played a key role in terrestrial adaptions in Amblyopinae, as well as in Oxudercinae, and provide new insights into the molecular mechanisms underlying the water-to-land transition in vertebrates.

Timing of organogenesis underscores the evolution of neonatal life histories and powered flight in bats.

Bats have undergone one of the most drastic limb innovations in vertebrate history, associated with the evolution of powered flight. Knowledge of the genetic basis of limb organogenesis in bats has increased but little has been documented regarding the differences between limb organogenesis in bats and that of other vertebrates. We conducted embryological comparisons of the timelines of limb organogenesis in 24 bat species and 72 non-bat amniotes. In bats, the time invested for forelimb organogenesis has been considerably extended and the appearance timing of the forelimb ridge has been significantly accelerated, whereas the timing of the finger and first appearance of the claw development has been delayed, facilitating the enlargement of the manus. Furthermore, we discovered that bats initiate the development of their hindlimbs earlier than their forelimbs compared with other placentals. Bat neonates are known to be able to cling continuously with their well-developed foot to the maternal bodies or habitat substrates soon after birth. We suggest that this unique life history of neonates, which possibly coevolved with powered flight, has driven the accelerated development of the hindlimb and precocious foot.

Comparative analysis reveals the long-term coevolutionary history of parvoviruses and vertebrates.

Parvoviruses (family Parvoviridae) are small DNA viruses that cause numerous diseases of medical, veterinary, and agricultural significance and have important applications in gene and anticancer therapy. DNA sequences derived from ancient parvoviruses are common in animal genomes and analysis of these endogenous parvoviral elements (EPVs) has demonstrated that the family, which includes twelve vertebrate-specific genera, arose in the distant evolutionary past. So far, however, such "paleovirological" analysis has only provided glimpses into the biology of ancient parvoviruses and their long-term evolutionary interactions with hosts. Here, we comprehensively map EPV diversity in 752 published vertebrate genomes, revealing defining aspects of ecology and evolution within individual parvovirus genera. We identify 364 distinct EPV sequences and show these represent approximately 200 unique germline incorporation events, involving at least five distinct parvovirus genera, which took place at points throughout the Cenozoic Era. We use the spatiotemporal and host range calibrations provided by these sequences to infer defining aspects of long-term evolution within individual parvovirus genera, including mammalian vicariance for genus Protoparvovirus, and interclass transmission for genus Dependoparvovirus. Moreover, our findings support a model of virus evolution in which the long-term cocirculation of multiple parvovirus genera in vertebrates reflects the adaptation of each viral genus to fill a distinct ecological niche. Our findings show that efforts to develop parvoviruses as therapeutic tools can be approached from a rational foundation based on comparative evolutionary analysis. To support this, we published our data in the form of an open, extensible, and cross-platform database designed to facilitate the wider utilisation of evolution-related domain knowledge in parvovirus research.

Lung evolution in vertebrates and the water-to-land transition.

A crucial evolutionary change in vertebrate history was the Palaeozoic (Devonian 419-359 million years ago) water-to-land transition, allowed by key morphological and physiological modifications including the acquisition of lungs. Nonetheless, the origin and early evolution of vertebrate lungs remain highly controversial, particularly whether the ancestral state was paired or unpaired. Due to the rarity of fossil soft tissue preservation, lung evolution can only be traced based on the extant phylogenetic bracket. Here we investigate, for the first time, lung morphology in extensive developmental series of key living lunged osteichthyans using synchrotron x-ray microtomography and histology. Our results shed light on the primitive state of vertebrate lungs as unpaired, evolving to be truly paired in the lineage towards the tetrapods. The water-to-land transition confronted profound physiological challenges and paired lungs were decisive for increasing the surface area and the pulmonary compliance and volume, especially during the air-breathing on land.

Metabolic Scaling in Birds and Mammals: How Taxon Divergence Time, Phylogeny, and Metabolic Rate Affect the Relationship between Scaling Exponents and Intercepts.

Simple SummaryThis study is based on a large dataset and re-evaluates data on the metabolic rate, providing new insights into the similarities and differences across different groups of birds and mammals. We compared six taxonomic groups of mammals and birds according to their energetic characteristics and the geological time of evolutionary origin. The overall metabolic rate of a taxonomic group increases with the geological time of evolutionary origin. The terrestrial mammals and flightless birds have almost equal metabolic levels. The higher the metabolic rate in a group, the less it increases within increasing body size in this group.Analysis of metabolic scaling in currently living endothermic animal species allowed us to show how the relationship between body mass and the basal metabolic rate (BMR) has evolved in the history of endothermic vertebrates. We compared six taxonomic groups according to their energetic characteristics and the time of evolutionary divergence. We transformed the slope of the regression lines to the common value and analyzed three criteria for comparing BMR of different taxa regardless of body size. Correlation between average field metabolic rate (FMR) of the group and its average BMR was shown. We evaluated the efficiency of self-maintenance in ordinary life (defined BMR/FMR) in six main groups of endotherms. Our study has shown that metabolic scaling in the main groups of endothermic animals correlates with their evolutionary age: the younger the group, the higher the metabolic rate, but the rate increases more slowly with increasing body weight. We found negative linear relationship for scaling exponents and the allometric coefficient in five groups of endotherms: in units of mL O2/h per g, in relative units of allometric coefficients, and also in level or scaling elevation. Mammals that diverged from the main vertebrate stem earlier have a higher “b” exponent than later divergent birds. A new approach using three criteria for comparing BMR of different taxa regardless of body mass will be useful for many biological size-scaling relationships that follow the power function.

Thyroid and endostyle development in cyclostomes provides new insights into the evolutionary history of vertebrates

BackgroundThe endostyle is an epithelial exocrine gland found in non-vertebrate chordates (amphioxi and tunicates) and the larvae of modern lampreys. It is generally considered to be an evolutionary precursor of the thyroid gland of vertebrates. Transformation of the endostyle into the thyroid gland during the metamorphosis of lampreys is thus deemed to be a recapitulation of a past event in vertebrate evolution. In 1906, Stockard reported that the thyroid gland in hagfish, the sister cyclostome group of lampreys, develops through an endostyle-like primordium, strongly supporting the plesiomorphy of the lamprey endostyle. However, the findings in hagfish thyroid development were solely based on this single study, and these have not been confirmed by modern molecular, genetic, and morphological data pertaining to hagfish thyroid development over the last century.ResultsHere, we showed that the thyroid gland of hagfish undergoes direct development from the ventrorostral pharyngeal endoderm, where the previously described endostyle-like primordium was not found. The developmental pattern of the hagfish thyroid, including histological features and regulatory gene expression profiles, closely resembles that found in modern jawed vertebrates (gnathostomes). Meanwhile, as opposed to gnathostomes but similar to non-vertebrate chordates, lamprey and hagfish share a broad expression domain of Nkx2-1/2-4, a key regulatory gene, in the pharyngeal epithelium during early developmental stages.ConclusionsBased on the direct development of the thyroid gland both in hagfish and gnathostomes, and the shared expression profile of thyroid-related transcription factors in the cyclostomes, we challenge the plesiomorphic status of the lamprey endostyle and propose an alternative hypothesis where the lamprey endostyle could be obtained secondarily in crown lampreys.

Mineralized Cartilage and Bone-Like Tissues in Chondrichthyans Offer Potential Insights Into the Evolution and Development of Mineralized Tissues in the Vertebrate Endoskeleton.

The impregnation of biominerals into the extracellular matrix of living organisms, a process termed biomineralization, gives rise to diverse mineralized (or calcified) tissues in vertebrates. Preservation of mineralized tissues in the fossil record has provided insights into the evolutionary history of vertebrates and their skeletons. However, current understanding of the vertebrate skeleton and of the processes underlying its formation is biased towards biomedical models such as the tetrapods mouse and chick. Chondrichthyans (sharks, skates, rays, and chimaeras) and osteichthyans are the only vertebrate groups with extant (living) representatives that have a mineralized skeleton, but the basal phylogenetic position of chondrichthyans could potentially offer unique insights into skeletal evolution. For example, bone is a vertebrate novelty, but the internal supporting skeleton (endoskeleton) of extant chondrichthyans is commonly described as lacking bone. The molecular and developmental basis for this assertion is yet to be tested. Subperichondral tissues in the endoskeleton of some chondrichthyans display mineralization patterns and histological and molecular features of bone, thereby challenging the notion that extant chondrichthyans lack endoskeletal bone. Additionally, the chondrichthyan endoskeleton demonstrates some unique features and others that are potentially homologous with other vertebrates, including a polygonal mineralization pattern, a trabecular mineralization pattern, and an unconstricted perichordal sheath. Because of the basal phylogenetic position of chondrichthyans among all other extant vertebrates with a mineralized skeleton, developmental and molecular studies of chondrichthyans are critical to flesh out the evolution of vertebrate skeletal tissues, but only a handful of such studies have been carried out to date. This review discusses morphological and molecular features of chondrichthyan endoskeletal tissues and cell types, ultimately emphasizing how comparative embryology and transcriptomics can reveal homology of mineralized skeletal tissues (and their cell types) between chondrichthyans and other vertebrates.

The fossil vertebrates of Guatemala

The fossil vertebrates of Guatemala are almost exclusively fossils of mammals and are of late Miocene (Hemphillian) and late Pleistocene (Rancholabrean) age. The only lower vertebrates are the crocodile fossil Crocodilus moreletti collected in the Río La Pasión area, a turtle from El Trifinio and fishes from Río Carboneras. The late Miocene mammals are the proboscidean Gomphotherium, an aceratheriine rhinoceros and the horse Neohipparion from the Río Carboneras in Izabal; the holotype of “Serridentinus guatemalensis” (nomen dubium) from Chinautla in the Department of Guatemala is also a specimen of Gomphotherium of likely late Miocene age. Late Pleistocene vertebrates are known from at least 36 localities in Guatemala, but only six of these yield at least four documented genera of mammals—Chivacabé, Ciudad Real. El Rosario, Estanzuela, Río La Pasión and San Rafaelito. The combined list of Guatemalan late Pleistocene mammal genera is Canis, Cuvieronius, Dicotyles, Equus, Eremotherium, Euceratherium, Glyptotherium, Holmesina, Mammuthus, Mazama, Megalonyx, Mixotoxodon, Neochoerus, Odocoileus, Pachyarmatherium, Palaeolama, Paramylodon, and Tapirus. The late Pleistocene mammals from Guatemala resemble broadly correlative mammal assemblages from throughout Central America in being dominated by the fragmentary remains of large herbivorous mammals and in having a mixture of immigrants from both North and South America. They thus well reflect a substantial taphonomic megabias in the Central American Pleistocene mammal record towards large mammals with large and durable skeletal parts that are easily preserved and readily discovered. This megabias renders problematic direct biological inferences from the Guatemalan Pleistocene mammal record. Mammoth records from Guatemala are relatively numerous for a Central American country but so few that inferring extensive grasslands or positing migration routs of mammoths from these records are questionable. There is no demonstrable association of humans with extinct Pleistocene megamammals in Guatemala despite claims to the contrary. The suggestion that during the late Pleistocene Guatemala was north of a biogeographic juncture between North and South America lacks any support. The Guatemalan fossil vertebrate record needs extensive augmentation, with an appropriate stratigraphic context, especially of lower vertebrates and micromammals, to provide further insight into vertebrate history in Central America during the last 10 million years.

Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution

Ancient polyploidization events have had a lasting impact on vertebrate genome structure, organization and function. Some key questions regarding the number of ancient polyploidization events and their timing in relation to the cyclostome-gnathostome divergence have remained contentious. Here we generate de novo long-read-based chromosome-scale genome assemblies for the Japanese lamprey and elephant shark. Using these and other representative genomes and developing algorithms for the probabilistic macrosynteny model, we reconstruct high-resolution proto-vertebrate, proto-cyclostome and proto-gnathostome genomes. Our reconstructions resolve key questions regarding the early evolutionary history of vertebrates. First, cyclostomes diverged from the lineage leading to gnathostomes after a shared tetraploidization (1R) but before a gnathostome-specific tetraploidization (2R). Second, the cyclostome lineage experienced an additional hexaploidization. Third, 2R in the gnathostome lineage was an allotetraploidization event, and biased gene loss from one of the subgenomes shaped the gnathostome genome by giving rise to remarkably conserved microchromosomes. Thus, our reconstructions reveal the major evolutionary events and offer new insights into the origin and evolution of vertebrate genomes.

From the river to the ocean: mitochondrial DNA analyses provide evidence of spectacled caimans (Caiman crocodilus Linnaeus 1758) mainland–insular dispersal

Abstract There are few studies that have investigated the evolutionary history of large vertebrates on islands off the Caribbean coast of South America. Here we use the spectacled caiman (Caiman crocodilus) to investigate among- and within-population patterns of genetic diversity to understand connectivity between island and mainland populations. The spectacled caiman is naturally distributed across Central and South America including the islands of Trinidad and Tobago, which are considered to have the only natural insular populations of the species. Because of this apparent isolation, we sought to determine whether caimans on Trinidad and Tobago comprise a unique lineage and have reduced genetic diversity compared to mainland caimans. We test these hypotheses by using mitochondrial DNA variation to assess the phylogenetic and phylogeographical relationships of the C. crocodilus populations inhabiting these islands within the evolutionary context of the entire spectacled caiman complex. Phylogenetic analyses placed the Trinidad and Tobago samples together with samples from Colombia, Venezuela and Brazil into one well-supported clade, which corresponds to the defined Orinoco/upper Negro lineage. Interestingly, the majority of sequences from Trinidad and Tobago are similar or identical to haplotypes reported from Venezuela and Colombia, supporting the idea of a dispersal process from the Orinoco River to these islands. We discuss the implications of our findings for systematics and the conservation of the species and how these dispersal movements could shape the current phylogeographical structure depicted for C. crocodilus.

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.