The petrosal bone and bony labyrinth of early to middle Miocene European deer (Mammalia,Cervidae) reveal their phylogeny

Deer (Cervidae) have a long evolutionary history dating back to the Early Miocene, around 19 million years ago. The best known fossils to document this history belong to European taxa, which all bear cranial appendages more or less similar to today's deer antlers. Despite the good fossil record, relationships of the earliest stem deer and earliest crown deer are much debated. This hampers precise calibration against the independent evidence of the fossil record in molecular clock analyses. While much has been written on the Early and Middle Miocene deer, only two phylogenetic analyses have been performed on these taxa to date mostly based on cranial appendage characters. Because the petrosal bone and bony labyrinth have been shown to be relevant for phylogeny in ruminants, we describe for the first time these elements for four iconic early cervids from Europe (Procervulus dichotomus, Heteroprox larteti, Dicrocerus elegans and Euprox furcatus) and include them in a phylogenetic analysis based on the ear region exclusively. The analysis recovered E. furcatus in a sister position to the living red deer (Cervus elaphus). Further, it placed D. elegans in a sister position to Euprox + Cervus and a clade Procervulinae that includes P. dichotomus and H. larteti, in sister position to all other deer. The inclusion of E. furcatus in crown Cervidae, which was previously suggested based on antler morphology, cannot be ruled out here but needs a more comprehensive comparison to other crown deer to be confirmed. J. Morphol. 277:1329–1338, 2016. © 2016 Wiley Periodicals, Inc.     

Evolution of electrosensory ampullary organs: conservation of Eya4 expression during lateral line development in jawed vertebrates

The lateral line system of fishes and amphibians comprises two ancient sensory systems: mechanoreception and electroreception. Electroreception is found in all major vertebrate groups (i.e. jawless fishes, cartilaginous fishes, and bony fishes); however, it was lost in several groups including anuran amphibians (frogs) and amniotes (reptiles, birds, and mammals), as well as in the lineage leading to the neopterygian clade of bony fishes (bowfins, gars, and teleosts). Electroreception is mediated by modified “hair cells,” which are collected in ampullary organs that flank lines of mechanosensory hair cell containing neuromasts. In the axolotl (a urodele amphibian), grafting and ablation studies have shown a lateral line placode origin for both mechanosensory neuromasts and electrosensory ampullary organs (and the neurons that innervate them). However, little is known at the molecular level about the development of the amphibian lateral line system in general and electrosensory ampullary organs in particular. Previously, we identified Eya4 as a marker for lateral line (and otic) placodes, neuromasts, and ampullary organs in a shark (a cartilaginous fish) and a paddlefish (a basal ray‐finned fish). Here, we show that Eya4 is similarly expressed during otic and lateral line placode development in the axolotl (a representative of the lobe‐finned fish clade). Furthermore, Eya4 expression is specifically restricted to hair cells in both neuromasts and ampullary organs, as identified by coexpression with the calcium‐buffering protein Parvalbumin3. As well as identifying new molecular markers for amphibian mechanosensory and electrosensory hair cells, these data demonstrate that Eya4 is a conserved marker for lateral line placodes and their derivatives in all jawed vertebrates.     

The phylogeny of aglaspidid arthropods and the internal relationships within Artiopoda

The phylogenetic position of aglaspidids, a problematic group of Lower Palaeozoic arthropods of undetermined affinities, is re‐examined in the context of the major Cambrian and Ordovician lamellipedian arthropod groups. A cladistic analysis of ten genera of aglaspidids sensu stricto, six aglaspidid‐like arthropods and 42 Palaeozoic arthropod taxa indicates that Xenopoda, Cheloniellida, Aglaspidida sensu lato and Trilobitomorpha form a clade (Artiopoda Hou and Bergström, 1997 ) nested within the mandibulate stem‐lineage, thus discarding previous interpretations of these taxa as part 'of the chelicerate stem‐group (Arachnomorpha Heider, 1913 ). The results confirm an aglaspidid identity for several recently described arthropods, including Quasimodaspis brentsae, Tremaglaspis unite, Chlupacaris dubia, Australaglaspis stonyensis and an unnamed Ordovician Chinese arthropod. The problematic Bohemian arthropod Kodymirus vagans was recovered as sister taxon to Beckwithia typa, and both form a small clade that falls outside Aglaspidida sensu stricto, thus discarding eurypterid affinities for the former. The analysis does not support the phylogenetic position of Kwanyinaspis maotianshanensis at the base of Conciliterga as proposed in recent studies, but rather occupies a basal position within Aglaspidida sensu lato. The results indicate a close association of aglaspidid arthropods with xenopods (i.e. Emeraldella and Sidneyia) and cheloniellids (e.g. Cheloniellon, Duslia); the new clade “Vicissicaudata” is proposed to encompass these arthropods, which are characterized by a differentiated posterior region. The phylogenetic position of aglaspidid arthropods makes them good outgroup candidates for analysing the internal relationships within the groups that form Trilobitomorpha. This work provides a much clearer picture of the phylogenetic relationships among Lower Palaeozoic lamellipedians.     

Comments on hexanchiform phylogeny (Pisces, Neoselachii)

The Hexanchiformes (Cow Sharks) are regarded as a monophyletic taxon. Cladistic analysis shows that among the various neoselachian taxa proposed so far as the sister group of the Hexanchiformes a sister group relationship between the Hexanchiformes and a (still unnamed) taxon comprising the Squaliformes and Pristiophoriformes appears as the most probable hypothesis. In addition, MAISEY and WOLFRAM'S (1984) concept of hexanchiform interrelationships is critically reviewed. An alternative cladogram of hexanchiform interrelationships is developed which includes Recent as well as fossil hexanchiform taxa. In this cladogram the living genera Hexancbus and Notorynchus are sister groups and both taxa together form the sister group of the Recent Heptranchias. The fossil taxa +Notidanoides, +“Hexanchus” gracilis, +Notidanodon and +Weltonia are arranged in the stem lineage of recent Hexanchiformes.     

The phylogenetic origin and evolution of acellular bone in teleost fishes: insights into osteocyte function in bone metabolism

Vertebrate bone is composed of three main cell types: osteoblasts, osteoclasts and osteocytes, the latter being by far the most numerous. Osteocytes are thought to play a fundamental role in bone physiology and homeostasis, however they are entirely absent in most extant species of teleosts, a group that comprises the vast majority of bony ‘fishes’, and approximately half of vertebrates. Understanding how this acellular (anosteocytic) bone appeared and was maintained in such an important vertebrate group has important implications for our understanding of the function and evolution of osteocytes. Nevertheless, although it is clear that cellular bone is ancestral for teleosts, it has not been clear in which specific subgroup the osteocytes were lost. This review aims to clarify the phylogenetic distribution of cellular and acellular bone in teleosts, to identify its precise origin, reversals to cellularity, and their implications. We surveyed the bone type for more than 600 fossil and extant ray‐finned fish species and optimised the results on recent large‐scale molecular phylogenetic trees, estimating ancestral states. We find that acellular bone is a probable synapomorphy of Euteleostei, a group uniting approximately two‐thirds of teleost species. We also confirm homoplasy in these traits: acellular bone occurs in some non‐euteleosts (although rarely), and cellular bone was reacquired several times independently within euteleosts, in salmons and relatives, tunas and the opah (Lampris sp.). The occurrence of peculiar ecological (e.g. anadromous migration) and physiological (e.g. red‐muscle endothermy) strategies in these lineages might explain the reacquisition of osteocytes. Our review supports that the main contribution of osteocytes in teleost bone is to mineral homeostasis (via osteocytic osteolysis) and not to strain detection or bone remodelling, helping to clarify their role in bone physiology.     

Aspects of the fossil record and phylogeny of the familyRutaceae (Zanthoxyleae,Toddalioideae)

A comparative analysis of the seed morphology and anatomy of fossil and extantRutaceae (mainlyZanthoxyleae andToddalioideae) is presented. This allows to place the most important fossil taxa in a time-table and on paleogeographical maps. A phylogenetic scheme demonstrates the postulated historical relationships ofEvodia, Zanthoxylum, Fagara, Rutaspermum, Acronychia, Toddalia, Fagaropsis, andPhellodendron.     

Different Level of Intraspecific Variation of the Bony Labyrinth Morphology in Slow- Versus Fast-Moving Primates

The vestibular system of the inner ear detects the motions of the head and is involved in maintaining balance. For this reason, this organ has been deeply studied and several scientists have tried to link its morphology with the locomotor behavior of an animal. Via high-resolution computed microtomography and geometric morphometric methods, we analyzed the intraspecific variation of the 3D morphology of the bony labyrinth (inner ear) in four species of primates differing in their locomotor adaptations: two being slow-moving taxa (Nycticebus and Perodicticus), and two being fast-moving taxa (Callithrix and Microcebus). Basically, there are very few analyses of the inter-individual variation of this organ in mammals in general, and this approach has never been attempted in primates thus far. Our results show that variation of the bony labyrinth morphology is expressed by the same ways in the different species (e.g., differences in the size, shape, and orientation of the semicircular canals, and in the width and height of the cochlea), but that slow-moving taxa exhibit a higher amount of intraspecific variation than do fast-moving taxa. Our results strengthen support for a previously published hypothesis, according to which a relaxation of the selective pressure applied to the morphology of the bony labyrinth is the likely reason for this higher amount of intraspecific variation in slow-moving taxa, and that it may be related to a reduced functional demand for rapid postural adjustments.     

Comparative anatomy of the bony labyrinth of extant and extinct porpoises (Cetacea: Phocoenidae)

The inner ear anatomy of cetaceans, now more readily accessible by means of nondestructive high‐resolution X‐ray computed tomographic (CT) scanning, provides a window into their acoustic abilities and ecological preferences. Inner ear labyrinths also may be a source for additional morphological characters for phylogenetic analyses. In this study, we explore digital endocasts of the inner ear labyrinths of representative species of extinct and extant porpoises (Mammalia: Cetacea: Phocoenidae), a clade of some of the smallest odontocete cetaceans, which produce some of the highest‐frequency clicks for biosonar and communication. Metrics used to infer hearing ranges based on cochlear morphology indicate that all taxa considered could hear high‐frequency sounds, thus the group had already acquired high‐frequency hearing capabilities by the Miocene (9–11 Mya) at the latest. Vestibular morphology indicates that extant species with pelagic preferences have similarly low semicircular canal deviations from 90°, values indicating more sensitivity to head rotations. Species with near‐shore preferences have higher canal deviation values, indicating less sensitivity to head rotations. Extending these analyses to the extinct species, we demonstrate a good match between those predicted to have coastal (such as Semirostrum cerutti) preferences and high canal deviation values. We establish new body length relationships based on correlations with inner ear labyrinth volume, which can be further explored among other aquatic mammals to infer body size of specimens consisting of fragmentary material.     

PHYLOGENY OF LOBOCHARACIUM (CHLOROPHYCEAE) AND ALLIES: A STUDY OF 18S AND 26S rDNA DATA1

The phylogenetic affinities of Lobocharacium coloradoense were investigated by analysis of combined 18S and 26S rDNA data. Results from both parsimony and likelihood methods supported a close alliance among Lobocharacium, Characiosiphon, and Characiochloris. These three taxa formed a clade near the base of the “Dunaliella” group within the chlamydomonad lineage. Protosiphon, which exhibits a siphonous habit similar to Characiosiphon and Lobocharacium, was not resolved as a close ally of the latter two taxa. The Lobocharacium alliance was characterized by the presence of an attachment pad associated with the nonmotile vegetative stage and pyrenoids that possess cytoplasmic invaginations. The pyrenoid feature is an ultrastructural trait that has now been observed in five different chlorophycean lineages. The Lobocharacium–Characiosiphon–Characiochloris clade is not predicted by any classifications of green algae. Additional taxon and data sampling need to be completed to resolve inconsistencies between the molecular phylogenetic evidence and at least some of the current family‐level taxa.     

Enigmatic ear stones: what we know about the functional role and evolution of fish otoliths

Otoliths in bony fishes play an important role in the senses of balance and hearing. Otolith mass and shape are, among others, likely to be decisive factors influencing otolith motion and thus ear functioning. Yet our knowledge of how exactly these factors influence otolith motion is incomplete. In addition, experimental studies directly investigating the function of otoliths in the inner ear are scarce and yield partly conflicting results. Herein, we discuss questions and hypotheses on how otolith mass and shape, and the relationship between the sensory epithelium and overlying otolith, influence otolith motion. We discuss (i) the state‐of‐the‐art knowledge regarding otolith function, (ii) gaps in knowledge that remain to be filled, and (iii) future approaches that may improve our understanding of the role of otoliths in ear functioning. We further link these functional questions to the evolution of solid teleost otoliths instead of numerous tiny otoconia as found in most other vertebrates. Until now, the selective forces and/or constraints driving the evolution of solid calcareous otoliths and their diversity in shape in teleosts are largely unknown. Based on a data set on the structure of otoliths and otoconia in more than 160 species covering the main vertebrate groups, we present a hypothetical framework for teleost otolith evolution. We suggest that the advent of solid otoliths may have initially been a selectively neutral ‘by‐product’ of other key innovations during teleost evolution. The teleost‐specific genome duplication event may have paved the way for diversification in otolith shape. Otolith shapes may have evolved along with the considerable diversity of, and improvements in, auditory abilities in teleost fishes. However, phenotypic plasticity may also play an important role in the creation of different otolith types, and different portions of the otolith may show different degrees of phenotypic plasticity. Future studies should thus adopt a phylogenetic perspective and apply comparative and methodologically integrative approaches, including fossil otoliths, when investigating otoconia/otolith evolution and their function in the inner ear.     

Feeding ecology of the deep‐bodied fish Dapedium (Actinopterygii,Neopterygii) from the Sinemurian of Dorset,England

Reconstructing the feeding ecology of fossil fishes can be difficult, but new mechanical approaches enable reasonably reliable inferences by comparison with living forms. Here, the feeding ecology of one of the most iconic and abundant actinopterygians of the Early Jurassic, Dapedium, is explored through detailed anatomical study and functional analyses of jaw mechanics. Mathematical models derived from modern teleost functional morphology are applied, to ascertain the transmission of force through the jaws of Dapedium. A number of features not previously identified in the genus are described, and the dentition is described in full for the first time. The analysis of the functional morphology of Dapedium, in combination with its jaw anatomy and dentition, indicates that the genus was well adapted to a durophagous feeding habit, although indirect evidence suggests a more generalist feeding mode. Being a generalist durophage may explain the success of the genus in the aftermath of the end‐Triassic extinction event and its radiation in the Early Jurassic, as indicated by the ubiquity of Dapedium fossils throughout the Lower Lias.     

Linking cranial morphology to prey capture kinematics in three cleaner wrasses: Labroides dimidiatus,Larabicus quadrilineatus,and Thalassoma lutescens

Cleaner fishes are well known for removing and consuming ectoparasites off other taxa. Observers have noted that cleaners continuously “pick” ectoparasites from the bodies of their respective client organisms, but little is known about the kinematics of cleaning. While a recent study described the jaw morphology of cleaners as having small jaw‐closing muscles and weak bite forces, it is unknown how these traits translate into jaw movements during feeding to capture and remove ectoparasites embedded in their clients. Here, we describe cranial morphology and kinematic patterns of feeding for three species of cleaner wrasses. Through high‐speed videography of cleaner fishes feeding in two experimental treatments, we document prey capture kinematic profiles for Labroides dimidiatus, Larabicus quadrilineatus, and Thalassoma lutescens. Our results indicate that cleaning in labrids may be associated with the ability to perform low‐displacement, fast jaw movements that allow for rapid and multiple gape cycles on individually targeted items. Finally, while the feeding kinematics of cleaners show notable similarities to those of “picker” cyprinodontiforms, we find key differences in the timing of events. In fact, cleaners generally seem to be able to capture prey twice as fast as cyprinodontiforms. We thus suggest that the kinematic patterns exhibited by cleaners are indicative of picking behavior, but that “pickers” may be more kinematically diverse than previously thought. J. Morphol. 276:1377–1391, 2015. © 2015 Wiley Periodicals, Inc.     

Anatomy and early development of the pectoral girdle,fin, and fin spine of sturgeons (Actinopterygii: Acipenseridae)

Acipenseriformes hold an important place in the evolutionary history of bony fishes. Given their phylogenetic position as extant basal Actinopterygii, it is generally held that a thorough understanding of their morphology will greatly contribute to the knowledge of the evolutionary history and the origin of diversity for the major osteichthyan clades. To this end, we examined comparative developmental series from the pectoral girdle in Acipenser fulvescens, A. medirostris, A. transmontanus, and Scaphirhynchus albus to document, describe, and compare ontogenetic and allometric differences in the pectoral girdle. We find, not surprisingly, broad congruence between taxa in the basic pattern of development of the dermal and chondral elements of the pectoral girdle. However, we also find clear differences in the details of structure and development among the species examined in the dermal elements, including the clavicle, cleithrum, supracleithrum, posttemporal, and pectoral‐fin spine. We also find differences in the internal fin elements such as the distal radials as well as in the number of fin rays and their association with the propterygium. Further, there are clear ontogenetic differences during development of the dermal and chondral elements in these species and allometric variation in the pectoral‐fin spine. The characters highlighted provide a suite of elements for further examination in studies of the phylogeny of sturgeons. Determining the distribution of these characters in other sturgeons may aid in further resolution of phylogenetic relationships, and these data highlight the role that ontogenetic and comparative developmental studies provide in systematics. J. Morphol. 276:241–260, 2015. © 2014 Wiley Periodicals, Inc.     

The phylogeny of the living and fossil Sphenisciformes (penguins)

We present the first phylogenetic analysis of the Sphenisciformes that extensively samples fossil taxa. Combined analysis of 181 morphological characters and sequence fragments from mitochondrial and nuclear genes (12S, 16S, COI, cytochrome b, RAG‐1) yields a largely resolved tree. Two species of the New Zealand Waimanu form a trichotomy with all other penguins in our result. The much discussed giant penguins Anthropornis and Pachydyptes are placed in two clades near the base of the tree. Stratigraphic and phylogenetic evidence suggest that some lineages of penguins attained very large body size rapidly and early in the clade's evolutionary history. The only fossil taxa that fall inside the crown clade Spheniscidae are fossil species assigned to the genus Spheniscus. Thus, extant penguin diversity is more accurately viewed as the product of a successful radiation of derived taxa than as an assemblage of survivors belonging to numerous lineages. The success of the Spheniscidae may be due to novel feeding adaptations and a more derived flipper apparatus. We offer a biogeographical scenario for penguins that incorporates fossil distributions and paleogeographic reconstructions of the Southern continent's positions. Our results do not support an expansion of the Spheniscidae from a cooling Continental Antarctica, but instead suggest those species that currently breed in that area are the descendants of colonizers from the Subantarctic. Many important divergence events in the clade Spheniscidae can instead be explained by dispersal along the paths of major ocean currents and the emergence of new islands due to tectonic events. © The Willi Hennig Society 2006.     

A combined evidence phylogenetic analysis of Anguimorpha (Reptilia: Squamata)

Anguimorpha is a clade of limbed and limbless squamates with ca. 196 extant species and a known fossil record spanning the past 130 million years. Morphology‐based and molecule‐based phylogenetic analyses disagree on several key points. The analyses differ consistently in the placements of monstersaurs (e.g. Gila Monsters), shinisaurs (Crocodile Lizards), the anguid Anniella (American Legless Lizards), carusioids (Knobby Lizards), and the major clades within Varanus (Monitor Lizards). Given different data sources with such different phylogenetic hypotheses, Anguimorpha is an excellent candidate for a combined phylogenetic analysis. We constructed a data matrix consisting of 175 fossil and extant anguimorphs, and 2281 parsimony‐informative characters (315 morphological characters and 1969 molecular characters). We analysed these data using the computer program TNT using the “new technology search” with the ratchet. Our result is novel and shows similarities with both morphological and molecular trees, but is identical to neither. We find that a global combined evidence analysis (GCA) does not recover a holophyletic Varanoidea, but omission of fossil taxa reveals cryptic molecular support for that group. We describe these results and others from global morphological analysis, extant‐only morphological analysis, molecular data‐only analyses, combined evidence analysis of extant taxa, and GCA. © The Willi Hennig Society 2010.     

Metrical analysis of the basicranium of extant hominoids and Australopithecus

The size and shape of the basicranium (seen in norma basilaris) in Homo, Gorilla, Pan, Pongo, and Australopithecus have been studied by recording the relative disposition of midline and bilateral bony landmarks. Fifteen linear measurements and two angles were used to relate the landmarks. The relatively longer and narrower cranial base of Gorilla, Pan, and Pongo is clearly contrasted with the wider, shorter cranial base in Homo sapiens. When the same observations were made on two “robust” and two “gracile” australopithecine crania, marked differences were found between the taxa. In the two “robust” specimens, the foramen magnum is located relatively further forward, and the axis of the petrous temporal bone is aligned more nearly with the coronal plane than in the two “gracile” crania. The implications of this apparent parallelism in basicranial morphology between Homo sapiens and the “robust” australopithecines are discussed.     

Testing the phylogenetic position of Cambrian pancrustacean larval fossils by coding ontogenetic stages

The study of ontogeny as an integral part of understanding the pattern of evolution dates back over 200 years, but only recently have ontogenetic data been explicitly incorporated into phylogenetic analyses. Pancrustaceans undergo radical ontogenetic changes. The spectacular upper Cambrian “Orsten” fauna preserves phosphatized fossil larvae, including putative crown‐group pancrustaceans with amazingly complete developmental sequences. The putative presence and nature of adult stages remains a source of debate, causing spurious placements in a traditional morphological analysis. We introduce a new coding method where each semaphoront (discrete larval or adult stage) is considered an operational taxonomic unit. This avoids a priori assumptions of heterochrony. Characters and their states are defined to identify changes in morphology throughout ontogeny. Phylogenetic analyses of semaphoronts produced possible relationships of each Orsten fossil to the crown‐group clade expected from morphology shared with extant larvae. Bredocaris is a member of the stem lineage of Thecostraca or (Thecostraca + Copepoda), and Yicaris and Rehbachiella are probably members of the stem lineage of Cephalocarida. These placements rely directly on comparisons between extant and fossil larval character states. The position of Phosphatocopina remains unresolved. This method may have broader applications to other phylogenetic problems which may rely on ontogenetically variable homology statements.     

Phylogenetic interrelationships of ginglymodian fishes (Actinopterygii: Neopterygii)

The Ginglymodi is one of the most common, though poorly understood groups of neopterygians, which includes gars, macrosemiiforms, and “semionotiforms.” In particular, the phylogenetic relationships between the widely distributed “semionotiforms,” and between them and other ginglymodians have been enigmatic. Here, the phylogenetic relationships between eight of the 11 “semionotiform” genera, five genera of living and fossil gars and three macrosemiid genera, are analysed through cladistic analysis, based on 90 morphological characters and 37 taxa, including 7 out-group taxa. The results of the analysis show that the Ginglymodi includes two main lineages: Lepisosteiformes and †Semionotiformes. The genera †Pliodetes, †Araripelepidotes, †Lepidotes, †Scheenstia, and †Isanichthys are lepisosteiforms, and not semionotiforms, as previously thought, and these taxa extend the stratigraphic range of the lineage leading to gars back up to the Early Jurassic. A monophyletic †Lepidotes is restricted to the Early Jurassic species, whereas the strongly tritoral species previously referred to †Lepidotes are referred to †Scheenstia. Other species previously referred to †Lepidotes represent other genera or new taxa. The macrosemiids are well nested within semionotiforms, together with †Semionotidae, here restricted to †Semionotus, and a new family including †Callipurbeckia n. gen. minor (previously referred to †Lepidotes), †Macrosemimimus, †Tlayuamichin, †Paralepidotus, and †Semiolepis. Due to the numerous taxonomic changes needed according to the phylogenetic analysis, this article also includes formal taxonomic definitions and diagnoses for all generic and higher taxa, which are new or modified. The study of Mesozoic ginglymodians led to confirm Patterson’s observation that these fishes show morphological affinities with both halecomorphs and teleosts. Therefore, the compilation of large data sets including the Mesozoic ginglymodians and the re-evaluation of several hypotheses of homology are essential to test the hypotheses of the Halecostomi vs. the Holostei, which is one of the major topics in the evolution of Mesozoic vertebrates and the origin of modern fish faunas.     

Phylogeny and biogeography of tetralophodont rodents of the tribe Oryzomyini (Cricetidae: Sigmodontinae)

Oryzomyini is the richest tribe among the Sigmodontine rodents, encompassing 32 living and extinct genera and including an increasing number of recently described species and genera. Some Oryzomyini are tetralophodont showing a reduction in the number of molar folds to four, while most taxa in this tribe retain the plesiomorphic pentalophodont state. We applied phylogenetic methods, molecular dating techniques and ancestral area analyses to members of an oryzomyini clade informally named ‘D’ in former studies and included related fossil tetralophodont forms. Based on 98 morphological characters and sequences of five gene fragments, we found that the tetralophodont condition is paraphyletic. Among living taxa, Pseudoryzomys is sister to Holochilus, and Lundomys is derived from a basal divergence. A clade formed by living Holochilus and the fossils Noronhomys and Carletonomys is sister to Holochilus primigenus, making Holochilus paraphyletic. Therefore, we describe a new genus that accommodates the fossil H. primigenus. Because trans‐Andean taxa currently share a common ancestor with taxa of cis‐Adean distribution, the northern Andes uplift may have worked as a postdispersal barrier. The tetralophodont lineages diverged during the Pliocene from a cis‐Andean ancestor, and the Great Plains in South America may have favoured the diversification of tetralophodont forms adapted to open habitats during the Pliocene.