Dental eruption in afrotherian mammals

Background  

Afrotheria comprises a newly recognized clade of mammals with strong molecular evidence for its monophyly. In contrast, morphological data uniting its diverse constituents, including elephants, sea cows, hyraxes, aardvarks, sengis, tenrecs and golden moles, have been difficult to identify. Here, we suggest relatively late eruption of the permanent dentition as a shared characteristic of afrotherian mammals. This characteristic and other features (such as vertebral anomalies and testicondy) recall the phenotype of a human genetic pathology (cleidocranial dysplasia), correlations with which have not been explored previously in the context of character evolution within the recently established phylogeny of living mammalian clades.     

Chromosome painting in the manatee supports Afrotheria and Paenungulata

Background  

Sirenia (manatees, dugongs and Stellar's sea cow) have no evolutionary relationship with other marine mammals, despite similarities in adaptations and body shape. Recent phylogenomic results place Sirenia in Afrotheria and with elephants and rock hyraxes in Paenungulata. Sirenia and Hyracoidea are the two afrotherian orders as yet unstudied by comparative molecular cytogenetics. Here we report on the chromosome painting of the Florida manatee.     

Phylogeny and conservation priorities of afrotherian mammals (Afrotheria,Mammalia)

Kuntner, M., May‐Collado, L. J. & Agnarsson, I. (2010). Phylogeny and conservation priorities of afrotherian mammals (Afrotheria, Mammalia). —Zoologica Scripta, 40, 1–15. Phylogenies play an increasingly important role in conservation biology providing a species‐specific measure of biodiversity – evolutionary distinctiveness (ED) or phylogenetic diversity (PD) – that can help prioritize conservation effort. Currently, there are many available methods to integrate phylogeny and extinction risk, with an ongoing debate on which may be best. However, the main constraint on employing any of these methods to establish conservation priorities is the lack of detailed species‐level phylogenies. Afrotheria is a recently recognized clade grouping anatomically and biologically diverse placental mammals: elephants and mammoths, dugong and manatees, hyraxes, tenrecs, golden moles, elephant shrews and aardvark. To date, phylogenetic studies have focused on understanding higher level relationships among the major groups within Afrotheria. Here, we provide a species‐level phylogeny of Afrotheria based on nine molecular loci, placing nearly 70% of the extant afrotherian species (50) and five extinct species. We then use this phylogeny to assess conservation priorities focusing on the widely used evolutionary distinctiveness and global endangeredness (EDGE) method and how that compares to the more recently developed PD framework. Our results support the monophyly of Afrotheria and its sister relationship to Xenarthra. Within Afrotheria, the basal division into Afroinsectiphilia (aardvark, tenrecs, golden moles and elephant shrews) and Paenungulata (hyraxes, dugongs, manatees and elephants) is supported, as is the monophyly of all afrotherian families: Elephantidae, Procaviidae, Macroscelididae, Chrysochloridae, Tenrecidae, Trichechidae and Dugongidae. Within Afroinsectiphilia, we recover the most commonly proposed topology (Tubulidentata sister to Afroscoricida plus Macroscelidea). Within Paenungulata, Sirenia is sister to Hyracoidea plus Proboscidea, a controversial relationship supported by morphology. Within Proboscidea, the mastodon is sister to the remaining elephants and the woolly mammoth sister to the Asian elephant, while both living elephant genera, Loxodonta and Elephas are paraphyletic. Top ranking evolutionarily unique species always included the aardvark, followed by several species of elephant shrews and tenrecs. For conservation priorities top ranking species always included the semi‐aquatic Nimba otter shrew, some poorly known species, such as the Northern shrew tenrec, web‐footed tenrec, giant otter shrew and Giant golden mole, as well as high profile conservation icons like Asian elephant, dugong and the three species of manatee. Conservation priority analyses were broadly congruent between the EDGE and PD methodologies. However, for certain species EDGE overestimates conservation urgency as it, unlike PD, fails to account for the status of closely related, but less threatened, species. Therefore, PD offers a better guide to conservation decisions.     

A retroposon analysis of Afrotherian phylogeny

Recent comprehensive studies of DNA sequences support the monophyly of Afrotheria, comprising elephants, sirenians (dugongs and manatees), hyraxes, tenrecs, golden moles, aardvarks, and elephant shrews, as well as that of Paenungulata, comprising elephants, sirenians, and hyraxes. However, phylogenetic relationships among paenungulates, as well as among nonpaenungulates, have remained ambiguous. Here we applied an extensive retroposon analysis to these problems to support the monophyly of aardvarks, tenrecs, and golden moles, with elephant shrews as their sister group. Regarding phylogenetic relationships in Paenungulata, we could characterize only one informative locus, although we could isolate many insertions specific to each of three lineages, namely, Proboscidea, Sirenia, and Hyracoidea. These data prompted us to reexamine phylogenetic relationships among Paenungulata using 19 nuclear gene sequences resulting in three different analyses, namely, short interspersed element (SINE) insertions, nuclear sequence analyses, and morphological cladistics, supporting different respective phylogenies. We concluded that these three lineages diverged very rapidly in a very short evolutionary period, with the consequence that ancestral polymorphism present in the last common ancestor of Paenungulata results in such incongruence. Our results suggest the rapid fixation of many large-scale morphological synapomorphies for Tethytheria; implications of this in relation to the morphological evolution in Paenungulata are discussed.     

Toothed whale monophyly reassessed by SINE insertion analysis: the absence of lineage sorting effects suggests a small population of a common ancestral species

Morphological data have indicated that toothed whales form a monophyletic group. However, research published in the last several years has made the issue of the monophyly or paraphyly of toothed whales a subject of debate. Our group previously characterized three independent loci in which SINE insertions were shared among dolphins and sperm whales, thus supporting the traditional, morphologically based hypothesis of toothed whale monophyly. Although in recent years a few additional molecular works proposed this topology, there is still skepticism over this monophyly from the view point of molecular systematics. When the phylogeny of rapidly radiated taxa is examined using the SINE method, it is important to consider the ascertainment bias that arises when choosing a particular taxon for SINE loci screening. To overcome this methodological problem specific to the SINE method, we examined all possible topologies among sperm whales, dolphins and baleen whales by extensively screening SINE loci from species of all three lineages. We characterized nine independent SINE loci from the genomes of sperm whales and dolphins, all of which cluster sperm whales and dolphins but exclude baleen whales. Furthermore, we characterized ten independent loci from baleen whales, all of which were amplified in a common ancestor of these whales. From these observations, we conclude that toothed whales form a monophyletic group and that no ancestral SINE polymorphisms hinder their phylogenetic assignment despite the short divergence times of the major lineages of extant whales during evolution. These results suggest that a small population of common ancestors of all toothed whales ultimately diverged into the lineages of sperm whales and dolphins.     

Extrinsic Snout Musculature in Afrotheria and Lipotyphla

As currently recognized, the mammalian order Lipotyphla contains six extant families: Chrysochloridae, Erinaceidae, Solenodontidae, Soricidae, Talpidae, and Tenrecidae. Although most mammalogists have accepted this taxon, the morphological support for Lipotyphla is relatively weak, and recent phylogenetic studies using molecular data have concluded that it is not monophyletic. Instead, these molecular studies place chrysochlorids and tenrecids in the proposed clade Afrotheria, together with aardvarks, elephants, elephant shrews, hyraxes, and sirenians. Despite strong molecular support, Afrotheria has received little or no morphological support. It was recently suggested that a mobile snout might be a morphological feature uniting afrotherians. To test this proposal, I dissected the extrinsic snout musculature in an assortment of lipotyphlan and afrotherian mammals. These muscles provide support for Lipotyphla but not for Afrotheria. The snout is moved by different muscles in different afrotherian taxa, suggesting that the mobile snout is not homologous across different afrotherian lineages. In contrast, lipotyphlans have a distinctive set of five snout muscles moving the snout tip that appears to be unique to these six families. In addition, in soricids and talpids, four of the five snout muscles originate posterior to the zygomatic arch, supporting sister-taxon status for these two lineages. Although the extrinsic snout musculature does not support Afrotheria as presently proposed, it is consistent with an Afrotheria that does not include chrysochlorids and tenrecids.     

Newly discovered young CORE-SINEs in marsupial genomes

Although recent mammalian genome projects have uncovered a large part of genomic component of various groups, several repetitive sequences still remain to be characterized and classified for particular groups. The short interspersed repetitive elements (SINEs) distributed among marsupial genomes are one example. We have identified and characterized two new SINEs from marsupial genomes that belong to the CORE-SINE family, characterized by a highly conserved "CORE" domain. PCR and genomic dot blot analyses revealed that the distribution of each SINE shows distinct patterns among the marsupial genomes, implying different timing of their retroposition during the evolution of marsupials. The members of Mar3 (Marsupialia 3) SINE are distributed throughout the genomes of all marsupials, whereas the Mac1 (Macropodoidea 1) SINE is distributed specifically in the genomes of kangaroos. Sequence alignment of the Mar3 SINEs revealed that they can be further divided into four subgroups, each of which has diagnostic nucleotides. The insertion patterns of each SINE at particular genomic loci, together with the distribution patterns of each SINE, suggest that the Mar3 SINEs have intensively amplified after the radiation of diprotodontians, whereas the Mac1 SINE has amplified only slightly after the divergence of hypsiprimnodons from other macropods. By compiling the information of CORE-SINEs characterized to date, we propose a comprehensive picture of how SINE evolution occurred in the genomes of marsupials.     

CetSINEs and AREs are not SINEs but are parts of cetartiodactyl L1

Short interspersed repetitive elements (SINEs) are widely distributed among the genomes of eukaryotes. We proposed previously that a SINE should be defined by the presence of a region homologous to a tRNA or to 7SL RNA, together with A-box and B-box promoter sequences, in order to distinguish SINEs from other short repetitive sequences, such as short segments of LINEs (long interspersed repetitive elements; Okada et al. Gene 205, 229–243, 1997). Numerous SINE sequences have been deposited to date in DNA databases. In some cases, however, designation of a particular sequence is problematic when the short repetitive sequence has been defined as a SINE without reference to the presence or absence of promoter elements specific for RNA polymerase III. We demonstrate here that four different sequences, namely, ARE1p, ARE2p, CetSINE1, and CetSINE2, each of which has been reported as a SINE, are, in fact, only partial sequences of members of a new subfamily of L1. We also demonstrate that members of this subfamily are distributed specifically among the genomes of cetartiodactyls. Received: 3 May 2000 / Accepted: 22 August 2000     

Genome Size: A Novel Genomic Signature in Support of Afrotheria

Molecular phylogenetic analyses suggest an emerging phylogeny for the extant Placentalia (eutherian) that radically departs from morphologically based constructions of the past. Placental mammals are partitioned into four supraordinal clades: Afrotheria, Xenarthra, Laurasiatheria, and Euarchontoglires. Afrotheria form an endemic African clade that includes elephant shrews, golden moles, tenrecs, aardvarks, hyraxes, elephants, dugongs, and manatees. Datamining databases of genome size (GS) shows that till today just one afrotherian GS has been evaluated, that of the aardvark Orycteropus afer. We show that the GSs of six selected representatives across the Afrotheria supraordinal group are among the highest for the extant Placentalia, providing a novel genomic signature of this enigmatic group. The mean GS value of Afrotheria, 5.3 ± 0.7 pg, is the highest reported for the extant Placentalia. This should assist in planning new genome sequencing initiatives. [Reviewing Editor: Dmitri Petrov]     

Foods and feeding habits of wild and captive Sirenia

The Sirenia along with the elephants and hyraxes form the Super-Order Paenungulata. They are the only fully aquatic mammalian herbivores and are represented by three species of manatees (Trichechidae), the dugong and the now extinct, Steller's sea cow (Dugongidae). Sirenians are non-ruminant herbivores that have specialized hind-gut fermentation in a large paired caecum at the juncture of the large and small intestines. The stomach is relatively small and is characterized by a unique cardiac gland which contains most of the digestive-enzyme secreting cells. Little is known of the digestive physiology of sirenians. The metabolic rate of the manatee is very low in comparison to other mammals and may even represent the lowest weight-specific metabolic rate for any mammal known. Metabolic rates for Dugong have not yet been determined. Foods and feeding habits of these species are reviewed both qualitatively and quantitatively. Manatees consume approximately 896 of their total body weight in aquatic plants daily, whereas the same value for the dugong is about 14%. Digestibilities of aquatic plants vary from 45 to 70% for manatees and a single in vitro measurement for Dugong was 83% for sea-grass. The chemical composition of various plants consumed by wild and captive sirenians are presented and their value in the nutritional ecoloev of the different species is discussed.     

Predicting mammalian SINE subfamily activity from A-tail length

Based on previous observations that newly inserted LINEs and SINEs have particularly long 3' A-tails, which shorten rapidly during evolutionary time, we have analyzed the rat and mouse genomes for evidence of recently inserted SINEs and LINEs. We find that the youngest predicted subfamilies of rodent identifier (ID) elements, a rodent-specific SINE derived from tRNA(Ala), are preferentially associated with A-tails over 50 bases in the rat genome, as predicted. Furthermore, these studies detected a subfamily of ID elements that has made over 15,000 copies that is younger than any previously reported ID subfamily. We use PCR analysis of genomic loci to demonstrate that all subfamily members tested inserted after the divergence of Rattus norvegicus from Rattus rattus. We also found evidence that the rodent B1 family of elements is much more active currently in mouse than in rat. These data provide useful estimates of recent activity from all of the mammalian retrotransposons, as well as allowing identification of the most recent insertions for use as population and speciation markers in those species. Both the current rat ID and mouse B1 elements that are active have small, specific interruptions in their 3' A-tail sequences. We suggest that these interruptions stabilize the length of the A-tails and contribute to the activity of these subfamilies. We present a model in which the dynamics of the 3' A-tail may be a central controlling factor in SINE activity.     

First application of the SINE (short interspersed repetitive element) method to infer phylogenetic relationships in reptiles: an example from the turtle superfamily Testudinoidea

Although turtles (order Testudines) constitute one of the major reptile groups, their phylogenetic relationships remain largely unresolved. Hence, we attempted to elucidate their phylogeny using the SINE (short interspersed repetitive element) method, in which the sharing of a SINE at orthologous loci is indicative of synapomorphy. First, a detailed characterization of the tortoise polIII/SINE was conducted using 10 species from eight families of hidden-necked turtles (suborder Cryptodira). Our analysis of 382 SINE sequences newly isolated in the present study revealed two subgroups, namely Cry I and Cry II, which were distinguishable according to diagnostic nucleotides in the 3' region. Furthermore, four (IA-ID) and five (IIA-IIE) different SINE types were identified within Cry I and Cry II subgroups, respectively, based on features of insertions/deletions located in the middle of the SINE sequences. The relative frequency of occurrence of the subgroups and the types of SINEs in this family were highly variable among different lineages of turtles, suggesting active differential retroposition in each lineage. Further application of the SINE method using the most retrotranspositionally active types, namely IB and IC, challenged the established phylogenetic relationships of Bataguridae and its related families. The data for 11 orthologous loci demonstrated a close relationship between Bataguridae and Testudinidae, as well as the presence of the three clades within Bataguridae. Although the SINE method has been used to infer the phylogenies of a number of vertebrate groups, it has never been applied to reptiles. The present study represents the first application of this method to a phylogenetic analysis of this class of vertebrates, and it provides detailed information on the SINE subgroups and types. This information may be applied to the phylogenetic resolution of relevant turtle lineages.     

SINEs and LINEs: symbionts of eukaryotic genomes with a common tail

Many SINEs and LINEs have been characterized to date, and examples of the SINE and LINE pair that have the same 3' end sequence have also increased. We report the phylogenetic relationships of nearly all known LINEs from which SINEs are derived, including a new example of a SINE/LINE pair identified in the salmon genome. We also use several biological examples to discuss the impact and significance of SINEs and LINEs in the evolution of vertebrate genomes.     

Retroposition of the AFC Family of SINEs (Short Interspersed Repetitive Elements) Before and During the Adaptive Radiation of Cichlid Fishes in Lake Malawi and Related Inferences About Phylogeny

Lake Malawi is home to more than 450 species of endemic cichlids, which provide a spectacular example of adaptive radiation. To clarify the phylogenetic relationships among these fish, we examined the presence and absence of SINEs (short interspersed repetitive elements) at orthologous loci. We identified six loci at which a SINE sequence had apparently been specifically inserted by retroposition in the common ancestor of all the investigated species of endemic cichlids in Lake Malawi. At another locus, unique sharing of a SINE sequence was evident among all the investigated species of endemic non-Mbuna cichlids with the exception of Rhamphochromis sp. The relationships were in good agreement with those deduced in previous studies with various different markers, demonstrating that the SINE method is useful for the elucidation of phylogenetic relationships among cichlids in Lake Malawi. We also characterized a locus that exhibited transspecies polymorphism with respect to the presence or absence of the SINE sequence among non-Mbuna species. This result suggests that incomplete lineage sorting and/or interspecific hybridization might have occurred or be occurring among the species in this group, which might potentially cause misinterpretation of phylogenetic data, in particular when a single-locus marker, such as a sequence in the mitochondrial DNA, is used for analysis. Received: 15 December 2000 / Accepted: 30 January 2001     

Early Tertiary mammals from North Africa reinforce the molecular Afrotheria clade

The phylogenetic pattern and timing of the radiation of mammals, especially the geographical origins of major crown clades, are areas of controversy among molecular biologists, morphologists and palaeontologists. Molecular phylogeneticists have identified an Afrotheria clade, which includes several taxa as different as tenrecs (Tenrecidae), golden moles (Chrysochloridae), elephant-shrews (Macroscelididae), aardvarks (Tubulidentata) and paenungulates (elephants, sea cows and hyracoids). Molecular data also suggest a Cretaceous African origin for Afrotheria within Placentalia followed by a long period of endemic evolution on the Afro-Arabian continent after the mid-Cretaceous Gondwanan breakup (approx. 105-25 Myr ago). However, there was no morphological support for such a natural grouping so far. Here, we report new dental and postcranial evidence of Eocene stem hyrax and macroscelidid from North Africa that, for the first time, provides a congruent phylogenetic view with the molecular Afrotheria clade. These new fossils imply, however, substantial changes regarding the historical biogeography of afrotheres. Their long period of isolation in Africa, as assumed by molecular inferences, is now to be reconsidered inasmuch as Eocene paenungulates and elephant-shrews are here found to be related to some Early Tertiary Euramerican 'hyopsodontid condylarths' (archaic hoofed mammals). As a result, stem members of afrotherian clades are not strictly African but also include some Early Paleogene Holarctic mammals.     

A family of short retroposons (Squam1) from squamate reptiles (Reptilia: Squamata): Structure,evolution, and correlation with phylogeny

Sequences of the SINE family specific to squamate reptiles have been isolated from the genomes of lacertid lizards and sequenced. These retroposons, which we called Squam1, are 360–390 bp long and contain a region similar to the tRNA gene sequence at the 5’ end. This family has also been detected in representatives of other reptile families (varanids, iguanids (Anolis), gekkonids, and snakes), being absent from the genomes of crocodiles as well as amphibians, birds, and mammals. The primary structures of Squam1 copies have been comprehensively analyzed and compared with GenBank sequences. The genomes of most taxa contain two to three SINE subfamilies with specific diagnostic features in their primary structures. Individual similarity between the copies within each taxon is about 85%, with intrageneric similarity being only slightly higher. A comparison of consensus sequences between different lizard families has shown that Squam1 may be a convenient phylogenetic marker for this group of reptiles, having a number of both apomorphic and more or less pronounced synapomorphic features. By this criterion, snakes slightly differ from lizards but obviously belong to the same clade. However, they show no special affinity to varanids as the putative closest relatives of snakes, compared to other lizards.     

A molecular phylogeny for the South African limbless lizard taxa of the subfamily Acontinae (Sauria: Scincidae) with special emphasis on relationships within Acontias

In the present study, relationships among three genera Acontias, Acontophiops, and Typhlosaurus, that comprise the South African limbless lizard subfamily Acontinae, were assessed with partial sequences of the 16S rRNA mitochondrial DNA gene. In addition, relationships within Acontias were further investigated using sequence data from the cytochrome oxidase I gene (COI). Maximum likelihood and maximum parsimony analyses of the 16S rRNA mtDNA data revealed that within this subfamily, Typhlosaurus is basal while Acontophiops and Acontias are sister taxa. Based on the 16S rRNA mtDNA data, the relationships within Acontias placed A. meleagris orientalis as the sister taxon of A. percivali tasmani, with A. m. orientalis lineacauda morph and A. m. meleagrus being the sister taxa to this group. The small-bodied skinks A. lineatus lineatus and A. l. tristis formed a monophyletic group, with the medium-bodied species A. gracilicauda gracilicauda being their sister taxon. Analyses of the COI gene for Acontias place A. m. orientalis as the sister taxon of A. p. tasmani with both A. meleagris meleagris and A. m. orientalis lineacauda being distinct. In contrast to the 16S rRNA mtDNA data, the COI data placed A. g. gracilicauda as the sister taxon to these medium-bodied species; while the subspecies status of the small-bodied taxa A. l. lineatus and A. l. tristis is reaffirmed. Combined analysis of both gene fragments for Acontias taxa recovered the same clades as found using only COI data. Systematic affinities in Acontias are discussed. These results indicate that Acontias is more species rich than previously thought.     

Anthracobunids from the Middle Eocene of India and Pakistan Are Stem Perissodactyls

Anthracobunidae is an Eocene family of large mammals from south Asia that is commonly considered to be part of the radiation that gave rise to elephants (proboscideans) and sea cows (sirenians). We describe a new collection of anthracobunid fossils from Middle Eocene rocks of Indo-Pakistan that more than doubles the number of known anthracobunid fossils and challenges their putative relationships, instead implying that they are stem perissodactyls. Cranial, dental, and postcranial elements allow a revision of species and the recognition of a new anthracobunid genus. Analyses of stable isotopes and long bone geometry together suggest that most anthracobunids fed on land, but spent a considerable amount of time near water. This new evidence expands our understanding of stem perissodactyl diversity and sheds new light on perissodactyl origins.