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A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships
Abstract
Higher-level relationships within, and the root of Placentalia, remain contentious issues. Resolution of the placental tree is important to the choice of mammalian genome projects and model organisms, as well as for understanding the biogeography of the eutherian radiation. We present phylogenetic analyses of 63 species representing all extant eutherian mammal orders for a new molecular phylogenetic marker, a 1.3kb portion of exon 26 of the apolipoprotein B (APOB) gene. In addition, we analyzed a multigene concatenation that included APOB sequences and a previously published data set (Murphy et al., 2001b) of three mitochondrial and 19 nuclear genes, resulting in an alignment of over 17kb for 42 placentals and two marsupials. Due to computational difficulties, previous maximum likelihood analyses of large, multigene concatenations for placental mammals have used quartet puzzling, less complex models of sequence evolution, or phylogenetic constraints to approximate a full maximum likelihood bootstrap. Here, we utilize a Unix load sharing facility to perform maximum likelihood bootstrap analyses for both the APOB and concatenated data sets with a GTR+Gamma+I model of sequence evolution, tree-bisection and reconnection branch-swapping, and no phylogenetic constraints. Maximum likelihood and Bayesian analyses of both data sets provide support for the superordinal clades Boreoeutheria, Euarchontoglires, Laurasiatheria, Xenarthra, Afrotheria, and Ostentoria (pangolins+carnivores), as well as for the monophyly of the orders Eulipotyphla, Primates, and Rodentia, all of which have recently been questioned. Both data sets recovered an association of Hippopotamidae and Cetacea within Cetartiodactyla, as well as hedgehog and shrew within Eulipotyphla. APOB showed strong support for an association of tarsier and Anthropoidea within Primates. Parsimony, maximum likelihood and Bayesian analyses with both data sets placed Afrotheria at the base of the placental radiation. Statistical tests that employed APOB to examine a priori hypotheses for the root of the placental tree rejected rooting on myomorphs and hedgehog, but did not discriminate between rooting at the base of Afrotheria, at the base of Xenarthra, or between Atlantogenata (Xenarthra+Afrotheria) and Boreoeutheria. An orthologous deletion of 363bp in the aligned APOB sequences proved phylogenetically informative for the grouping of the order Carnivora with the order Pholidota into the superordinal clade Ostentoria. A smaller deletion of 237-246bp was diagnostic of the superordinal clade Afrotheria.
... However, branching within the Paenungulata is still debated (a phylogenetic time tree is provided in Figure 1). Rapid radiation, a deep divergence, and an extensive morphological diversification has led to limited phylogenetic signal confounding resolution at morphological and nucleotide levels (Amrine- Madsen et al., 2003;Kellogg et al., 2007;Nishihara et al., 2005;Pardini et al., 2007;Seiffert, 2007). Based on nine molecular loci, Sirenia is sister to Hyracoidea plus Proboscidea , whereas morphological evidence supports a Sirenian-Proboscidean clade (Tethytheria) within Paenungulata (Tassy & Shoshani, 1988). ...
... Tethytheria (Proboscidea and Sirenia) is accepted by Asher et al. (2003), Kjer and Honeycutt (2007), and Seiffert (2007). Other researchers reject Tethytheria in favor of a Hyracoidea-Sirenia clade (Matthee et al., 2007;Springer & Murphy, 2007) or reject Tethytheria because of a suggested Hyracoidea-Proboscides clade (Amrine- Madsen et al., 2003). ...
Vocal production learning is the ability to modify a vocal output in response to auditory experience. It is essential for human speech production and language acquisition. Vocal learning evolved independently several times in vertebrates, indicating evolutionary pressure in favor of this trait. This enables cross-species comparative analysis to be used to test evolutionary hypotheses. Humans share this ability with a versatile but limited group of species: songbirds, parrots and hummingbirds, bats, cetaceans, seals, and elephants. Although case studies demonstrate that African savanna and Asian elephants are capable of heterospecific imitation, including imitation of human words, our understanding of both the underlying mechanisms and the adaptive relevance within the elephant’s natural communication system is limited. Even though comparing phylogenetically distant species is intriguing, it is also worthwhile to investigate whether and to what extent learned vocal behavior is apparent in species phylogenetically close to an established vocal learner. For elephants, this entails determining whether their living relatives share their special ability for (complex) vocal learning.
In this review, we address vocal learning in Elephantidea and Sirenia, sister groups within the Paenungulata. So far, no research has been done on vocal learning in Sirenians. Because of their aquatic lifestyle, vocalization structure, and evolutionary relationship to elephants, we believe Sirenians are a particularly interesting group to study. This review covers the most important acoustic aspects related to vocal learning in elephants, manatees, and dugongs, as well as knowledge gaps that must be filled for one to fully comprehend why vocal learning evolved (or did not) in these distinctive but phylogenetically related taxa.
... Sirenia is a monophyletic order of mammals included in the superorder Afrotheria Stanhope et al., 1998, a clade well supported by molecular and genomic data (Amrine-Madsen et al., 2003;Murphy et al., 2004;Springer et al., 2015), which encompasses the extant placental mammals that originated in Africa: Tenrecoidea, Macroscelidea, Tubulidentata, Proboscidea, Hyracoidea and Sirenia (Tabuce et al., 2008). Within this superorder, the sirenians, proboscideans and hyracoideans form the clade Paenungulata Simpson, 1945, which is also broadly accepted on the basis of chromosomal studies (e.g. ...
... Nevertheless, this group is subject to controversy based on genetic studies (e.g. Ozawa et al., 1997;Amrine-Madsen et al., 2003;Kellogg et al., 2007;Pardini et al., 2007;Springer & Murphy, 2007;Seiffert, 2007). Although there is a reasonable consensus concerning the phylogenetic relationships of the order Sirenia, the contents remain unclear, and various phylogenetic proposals exist, especially for the Eocene taxa. ...
The pan-sirenian Bauplan is conservative, probably owing to the constraints of adaptation to an aquatic lifestyle. Gathering morphological data from extinct forms is complex, resulting in poorly resolved phylogenies for stem pansirenians. Extant sirenians ossify the falx cerebri and the tentorium cerebelli, membranes of the dura mater of the brain attached to the parietal bone. Nevertheless, these ossifications are not present in some pan-sirenians. The basioccipital bone has received little attention in the literature except for establishing the relative age of individuals. Here, we present new cranial elements and a detailed description of the skull of Sobrarbesiren cardieli, a stem pan-sirenian from the Lutetian of Spain represented by eight individuals; we study its intraspecific variation and
palaeoecological implications and explore the evolution of the endocranial structures and the basioccipital bone in pan-sirenians. Six new phylogenetic characters are added to the latest pan-sirenian dataset, resulting in a wellresolved topology where Sobrarbesiren is recovered close to the root, in a clade with Prototherium and Eotheroides aegyptiacum. The basioccipital bone and the ossified endocranial membranes have a phylogenetic signal, and the absence of such endocranial structures represents the plesiomorphic condition for pan-sirenians and is not diagnostic for the family Protosirenidae as previously believed.
... Прочие исследования демонстрируют монофилию «Eulipotyphla» (рис. 2,; при этом одни отвергают традиционное деление на Soricomorpha (в составе Soricidae, Talpidae и Solenodontidae) и Erinaceomorpha (Douady et al., 2002b;Jow et al., 2002;Malia et al., 2002;Amrine-Madsen et al., 2003;Douady, Douzery, 2003;Springer et al., 2003;Waddell, Shelley, 2003;Roca et al., 2004), а другие поддерживают его (Nikaido et al., 2001(Nikaido et al., , 2003см. также Symonds, 2005). ...
... По некоторым молекулярно-генетическим данным предполагается, что предковая группа Talpidae обособилась еще до разделения предков Erinaceidae и Soricidae (см. Douady et al., 2002b;Jow et al., 2002;Malia et al., 2002;Amrine-Madsen et al., 2003;Douady, Douzery, 2003;Springer et al., 2003;Waddell, Shelley, 2003). С учетом данных о еще большей древности Solenodontidae (Waddell, Shelley, 2003;Roca et al., 2004) и изолированном положении тенрекоидов, эта гипотеза полностью разрушает концепцию Soricomorpha -как в понимании У. Грегори (Gregory, 1910: Soricidae+Talpidae), так и в более широком понимании П. Батлера (Butler, 1972) или М. Маккенны (McKenna, 1975. ...
The article is devoted to the problem of the comparison of the newest data on the Early Paleogene insectivores and modern conceptions (including molecular genetic) of the classification of the group Lipotyphla. The analysis of evolutionary modifications of the dentition gave the basis for the discerning of the successive structural types of insectivore molars: (1) protodilambdomorph (primitive dilambdomorph) → protozalambdomorph (primitive tenrecoid zalambdomorph) → euzalambdomorph (advanced tenrecoid zalambdomorph); (2) protodilambdomorph → eudilambdomorph (advanced dilambdomorph) → parazalambdomorph (solenodontoid zalambdomorph); (3) protodilambdomorph or early eudilambdomorph → metadilambdomorph (nesophontoid dilambdomorph). The hypothetical scenario of the evolution of the group is proposed on the base of the total of the fundamentally compatible data.
... The mitochondrial gene COI (551 bp) [39] was amplified to access the maternal inheritance of the canid. Biparental inheritance was accessed using amplifying five nuclear segments, APOB (889 bp) [40], BDNF (542 bp) [41], CHRNA1 (339 bp) [42], GHR (749 bp), and FES (407 bp) [43], previously successfully amplified for South America canids [44]. PCR mix was performed with 1 µL of DNA (50 ng/µL), 0.2 µL of 10 mM forward and reverse primers, 0.2 µL of 10 mM deoxynucleotide triphosphates, 2.0 µL of 10X PCR buffer, 1.5 µL of 50 mM MgCl 2 polymerase cofactor, and 0.2 µL of 5 U/µL DNA Taq polymerase (Ludwig Biotec, Alvorada, Brazil), for 20 µL in total with the addition of ultrapure water. ...
Hybridization between species with different evolutionary trajectories can be a powerful threat to wildlife conservation. Anthropogenic activities, such as agriculture and livestock, have led to the degradation and loss of natural habitats for wildlife. Consequently, the incidence of interspecific hybridization between wild and domestic species has increased, although cases involving species of different genera are rare. In Vacaria, a Southern city in Brazil, a female canid with a strange phenotype, which had characteristics between the phenotype of the domestic dog (Canis familiaris) and that of the pampas fox (Lycalopex gymnocercus), was found. Our analysis suggests that the animal is a hybrid between a domestic dog and a pampas fox, but future studies are necessary to investigate additional cases of this hybridization in nature. This finding worries for the conservation of wild canids in South America, especially concerning Lycalopex species. Hybridization with the domestic dog may have harmful effects on pampas fox populations due to the potential for introgression and disease transmission by the domestic dog. Therefore, future studies to explore the consequences of hybridization on genetics, ecology, and behavior of wild populations will be essential to improve the conservation of this species.
... All the gene fragments were amplified with published primers (Table 3; Amrine-Madsen et al., 2003;Irwin et al., 1991;Lindblad-Toh et al., 2005;Murphy et al., 2000;Murphy et al., 2001). PCR amplifications were carried out in a reaction volume mixture of 25 μL containing 12.5 μL 2× Taq Master Mix (Vazyme), 1 μL each primer, 1 μL genomic DNA, and 9.5 μL double-distilled water. ...
The lacked-teeth pygmy weasel, Mustela aistoodonnivalis Wu & Kao, 1991, was originally described as being from Taibai Mountain and Zhashui county, Shaanxi, China.
Subsequently, it was considered a subspecies or synonym of Mustela nivalis. In a faunal survey of northwestern Sichuan, eight specimens of M. aistoodonnivalis were collected. A molecular phylogenetic analysis of one mitochondrial and six nuclear genes clustered the specimens as a distinct clade and not with M. nivalis. Morphologically, the lack of the second lower molar differentiated them from M. nivalis, and genetic distances were typical of discrete species. These analyses confirmed that M. aistoodonnivalis is an independent species in the genus Mustela.
... Mapping which features of the sleep spindle are universal versus species-specific will be crucial for reconstructing its evolution. One complication towards making the next step is the different results obtained using different methodologies for determining phylogenies in mammals (Amrine-Madsen et al., 2003;Reyes et al., 2004;Cannarozzi, Schneider & Gonnet, 2007;Helgen, 2011). For now, by using wellvalidated model species as a limited source of inference, we can demonstrate that some observations (Nicol et al., 2000;Zepelin et al., 2005;Voirin et al., 2014) about how sleep spindles are expressed across the animal kingdom are likely erroneous. ...
Sleep spindles are phasic events observed in mammalian non-rapid eye movement sleep. They are relevant today in the study of memory consolidation, sleep quality, mental health and ageing. We argue that our advanced understanding of their mechanisms has not exhausted the utility and need for animal model work. This is both because some topics, like cognitive ageing, have not yet been addressed sufficiently in comparative efforts and because the evolutionary history of this oscillation is still poorly understood. Comparisons across species often are either limited to referencing the classical cat and rodent models, or are over-inclusive, uncritically including reports of sleep spindles in rarely studied animals. In this review, we discuss the emergence of new (dog and sheep) models for sleep spindles and compare the strengths and shortcomings of new and old models based on the three validation criteria for animal models-face, predictive, and construct validity. We conclude that an emphasis on cognitive ageing might dictate the future of comparative sleep spindle studies, a development that is already becoming visible in studies on dogs. Moreover, reconstructing the evolutionary history of sleep spindles will require more stringent criteria for their identification, across more species. In particular, a stronger emphasis on construct and predictive validity can help verify if spindle-like events in other species are actual sleep spindles. Work in accordance with such stricter validation suggests that sleep spindles display more universally shared features, like defining frequency, than previously thought.
... Simpson, 1945;Novacek, 1992;Murphy et al., 2001;Arnason et al., 2002;Janečka et al., 2007;Meredith et al., 2011;Song et al., 2012). Also part of the Euarchontoglires are the taxa that constitute the Eurarchonta (Adkins & Honeycutt, 1991;Murphy et al., 2001;Springer et al., 2004;Bininda-Emonds et al, 2007; but see Amrine-Madsen et al., 2003). The Eurarchonta are hypothesized to include the Dermoptera (colugos), the Scandentia (treeshrews) and the Primates (monkeys, apes and humans). ...
Despite differences in the assumed ecological context in competing evolutionary scenarios for early primate locomotion, there appears to be consensus about the adaptive significance of grasping for the exploitation of the terminal branch habitat. I attempt to review first the phylogenetic framework of early primate evolution. Then, I focus on proposed extant analogues for potential ancestral morphotypes of early primate evolution and motion analyses conducted to gain insight specifically into the role of grasping during small-branch locomotion. Studies concerned with proposed extant analogues, such as treeshrews, didelphid marsupials, mouse lemurs, tamarins and marmosets, marsupial gliders and various small arboreal rodents, are summarized. This overview demonstrates a striking variability and plasticity of strategies to cope with the challenging functional demands of locomotion in the terminal branch habitat and helps to identify open questions for further research. For example, potential morphological correlates for specific behaviours still need to be validated in future in-depth quantitative experimental studies. Comparative approaches beyond the anatomy that specifically account for data on locomotor and postural behaviour of extant species, also including phylogenetically informed analyses, are mostly lacking and should be intended to link evolutionary patterns of morphological change with functional characteristics observed in experimental studies.
... This sister group relationship is recovered in some other phylogenetic analyses based on molecular data (Kjer & Honeycutt, 2007;Murphy et al., 2007), and supported by a feature of the internal carotid artery (Asher, 2001), but this is not a common result (Asher & Seiffert, 2010). Rather, in many phylogenies, Tenrecidae and Chrysochloridae are united in Afrosoricida (Stanhope et al., 1998;Springer et al., 1999;Murphy et al., 2001aMurphy et al., , 2001bAmrine-Madsen et al., 2003;Asher et al., 2003;Waddell & Shelley, 2003;Seiffert, 2007;O'Leary et al., 2013). The "fossorial" clade resulting from the first analysis of all mammals ( Figure 2) suggests a functional signal in the myology, so it seems wise to consider the myological features shared by Orycteropus and both Tenrecidae and Chrysochloridae. ...
... This sister group relationship is recovered in some other phylogenetic analyses based on molecular data (Kjer & Honeycutt, 2007;Murphy et al., 2007), and supported by a feature of the internal carotid artery (Asher, 2001), but this is not a common result (Asher & Seiffert, 2010). Rather, in many phylogenies, Tenrecidae and Chrysochloridae are united in Afrosoricida (Stanhope et al., 1998;Springer et al., 1999;Murphy et al., 2001aMurphy et al., , 2001bAmrine-Madsen et al., 2003;Asher et al., 2003;Waddell & Shelley, 2003;Seiffert, 2007;O'Leary et al., 2013). The "fossorial" clade resulting from the first analysis of all mammals ( Figure 2) suggests a functional signal in the myology, so it seems wise to consider the myological features shared by Orycteropus and both Tenrecidae and Chrysochloridae. ...
We present observations of the occurrence of sengis (Macroscelidea) in the Taratibu Reserve (Reserva de Taratibu), Quirimbas National Park, Northern Mozambique, along with notes on their habitat associations. Based upon field observations and trapping, we found Rhynchocyon cirnei and Petrodromus tetradactylus to occur in the Taratibu Reserve. Rhynchocyon cirnei was present in closed canopy Warnekea sp. and Parkinsonia sp. bush, and inselberg vegetation habitats. Petrodromus tetradactylus was also present in closed canopy Warnekea sp. and Parkinsonia sp. bush. This information is a new local record for each species and extends their confirmed distributions further south-west in the Quirimbas National Park.
... Furthermore, Apo A-I has been shown to have a regulatory role in the complement system by affecting membrane attach complex (MAC) assembly (Jenne et al., 1991;Hamilton et al., 1993;French et al., 1994). ApoB-100 is conserved between cetacean and other mammals (Amrine-Madsen et al., 2003), synthesised by the liver and plays parts of innate immune responses (Peterson et al., 2008). ApoB-100 is furthermore associated with ER stress and insulin resistance (Su et al., 2009) as well as lipid metabolism disorders (Andersen et al., 2016). ...
... Simpson, 1945;Novacek, 1992;Murphy et al., 2001;Arnason et al., 2002;Janečka et al., 2007;Meredith et al., 2011;Song et al., 2012). Also part of the Euarchontoglires are the taxa that constitute the Eurarchonta (Adkins & Honeycutt, 1991;Murphy et al., 2001;Springer et al., 2004;Bininda-Emonds et al, 2007; but see Amrine-Madsen et al., 2003). The Eurarchonta are hypothesized to include the Dermoptera (colugos), the Scandentia (treeshrews) and the Primates (monkeys, apes and humans). ...
Despite differences in the assumed ecological context in competing evolutionary scenarios for early primate locomotion, there appears to be consensus about the adaptive significance of grasping for the exploitation of the terminal branch habitat. I attempt to review first the phylogenetic framework of early primate evolution. Then, I focus on proposed extant analogues for potential ancestral morphotypes of early primate evolution and motion analyses conducted to gain insight specifically into the role of grasping during small-branch locomotion. Studies concerned with proposed extant analogues, such as treeshrews, didelphid marsupials, mouse lemurs, tamarins and marmosets, marsupial gliders and various small arboreal rodents, are summarized. This overview demonstrates a striking variability and plasticity of strategies to cope with the challenging functional demands of locomotion in the terminal branch habitat and helps to identify open questions for further research. For example, potential morphological correlates for specific behaviours still need to be validated in future in-depth quantitative experimental studies. Comparative approaches beyond the anatomy that specifically account for data on locomotor and postural behaviour of extant species, also including phylogenetically informed analyses, are mostly lacking and should be intended to link evolutionary patterns of morphological change with functional characteristics observed in experimental studies.
... This has implications for understanding how marsupials dispersed and evolved in Gondwana (e.g., Beck 2012). Australidelphia is supported by morphological evidence, predominantly from the ankle (Szalay 1982(Szalay , 1994, as well as cranial and dental findings (Horovitz and Sánchez-Villagra 2003), and molecular data (Amrine-Madsen et al. 2003;Beck 2008;Meredith et al. 2008). ...
We have analyzed the internal structure of the brain of the microbiotherian marsupial Dromiciops gliroides and compared it with the brains of American and Australian marsupials. Dromiciops does not have a fasciculus aberrans, but does exhibit other features of brain structure that are similar to diprotodontid metatherians (e.g., lamination of the lateral geniculate nucleus of the dorsal thalamus). Cortical organization in Dromiciops shows some similarities with that in Australian marsupial carnivores in that the proportional areas of isocortex devoted to somatosensory and visual function are similar in size to each other, and greater in area than that devoted to olfactory or auditory function. This points to similar sensory requirements for the foraging lifestyle of Dromiciops and small Australian marsupial carnivores, with isocortical specialization for somatosensation and vision. We also examined phylogenetic relationships of Dromiciops with extant marsupials based on maximum parsimony analysis using a soft body brain morphology-only matrix, representing 93 extant marsupial taxa. The results recovered Dromiciops as a sister group to the Australasian marsupial clade Diprotodontia.
... Anthracotheridae como um grupo irmão dos Cetáceos e propuseram a recente ordem Cetartiodactyla (Boisserie et al. 2005, Theodor 2004, Amrine-Madsen et al. 2003. A prévia ordem Artiodactyla é composta por três subordens: Tylopoda (camelos e lamas), Suiformes (porcos e "peccaries") e Ruminantia (antílopes, veados, girafas, bovinos, caprinos e ovinos) (Feldhamer et al. 2004) (cf. ...
ORGANIZATION AND EVOLUTION OF THE CARNIVORA GENOME: Felis catus
REPETITIVE FRACTION AND CHROMOSOMAL ARCHITECTURE
ABSTRACT: Modern felids appeared in the Superior Miocene and are today, one of the more
successful Carnivora families, what could maybe be the reflex of its remarkable genome conservation.
The major goals of this work were the genome organization comparative analysis and its
evolutionary dynamics in the Carnivora species, the cat (Felis catus), through the comparative
analysis of several DNA satellite families isolated from the cat genome, and the investigation of the
chromosomal architecture by “Comparative Chromosome Painting”.
In the first part of the work we analyzed the constitutive heterochromatin of Felis catus
genome, namely telomeres and three satellite DNA sequences (FA-SAT, AluI-Sat-1 and AluI-Sat-2).
The detailed analysis of the FA-SAT revealed the existence of integrated telomeric repetitive motifs.
Physical mapping of FA-SAT demonstrated its location at the telomeric regions and, for the first time,
its intersitial location on chromosome F1, what allowed the deduction of an important evolutionary
rearrangement (pericentric inversion) occurred during the evolution of Felis catus, and the dating of
the FA-SAT sequence, as having, at least, 55 million years. It was even suggested the physical
mapping of FA-SAT as a tool to evaluate the evolutionary status of Carnivora chromosomes and
karyotypes. The molecular investigation of the sequence AluI-Sat-2 revealed its non relation to the
other isolated sequences. Physical mapping on chromosomes and the nuclear topology and interphase
3D projections with simultaneous hybridization of the sequences AluI-Sat-2 and FA-SAT showed
that these sequences are mainly co-localized. The finding of different and non related sequences at the
same chromosomal regions is a surprising achievement that suggests an atypical nuclear organization
in what respects the repetitive fraction on the Felis catus genome.
Carnivora order is characterized by the existence of different patterns of genome
conservation/divergence. The different families exhibit different modes of chromosomal evolution,
being the Felidae karyotype significantly conserved throughout million years of evolution. In this
work we present a comparative partial chromosome map between Felis catus and Canis familiaris
(the two species in the extremes of the Carnivora chromosome spectrum and maybe on the Eutheria
one, in what concerns conservation/divergenece, number of chromosomal rearrangements and
chromosome number), using as “outgroups” the genomes of Ovis aries and Giraffa camelopardalis
(Cetartiodactyla). This is the first comparative genome map between the orders Cetartiodactyla and
Carnivora (with Cetartiodactyla probes). The conclusion of this map will be a major goal in the
visualization of the chromosomal events occurred during the course of evolution of Carnivora.
... There are eight mammal species shared by these two phylogenies, and all of the shared branches for these eight species agree with each other. Moreover, two lowest bootstrap scores (68, 71) on the middle two branches in the tree of Fig. 4 reflect the current controversial opinions in placing primates closer to rodents or carnivores [27][28][29][30][31][32]. ...
Background
Gene order changes, under rearrangements, insertions, deletions and duplications, have been used as a new type of data source for phylogenetic reconstruction. Because these changes are rare compared to sequence mutations, they allow the inference of phylogeny further back in evolutionary time. There exist many computational methods for the reconstruction of gene-order phylogenies, including widely used maximum parsimonious methods and maximum likelihood methods. However, both methods face challenges in handling large genomes with many duplicated genes, especially in the presence of whole genome duplication.
Methods
In this paper, we present three simple yet powerful methods based on maximum-likelihood (ML) approaches that encode multiplicities of both gene adjacency and gene content information for phylogenetic reconstruction.
Results
Extensive experiments on simulated data sets show that our new method achieves the most accurate phylogenies compared to existing approaches. We also evaluate our method on real whole-genome data from eleven mammals. The package is publicly accessible at http://www.geneorder.org.
Conclusions
Our new encoding schemes successfully incorporate the multiplicity information of gene adjacencies and gene content into an ML framework, and show promising results in reconstruct phylogenies for whole-genome data in the presence of massive duplications.
... The karyotype of Hoffmann's two-toed sloth is arranged from left to right in the order of chromosomal number, the number in the column refers to the number of HSA it is syntenic to, and the diagram below karyotype of ancestral placental mammals describes the synteny blocks in sloth chromosome. We can find that both are quite similar but one is subject to two fissions and one fusion, modified from Ref. [7]. which includes orders Eulipotyphla, Carnivora, Pholidota, Perissodactyla, Cetartiodactyla and Chiroptera; (3) Euarchontoglires, which includes Rodentia, Lagomorpha, Primates, Scandentia and Dermoptera; and (4) Xenarthra [8]. Currently, there are disputes and uncertainties in the phylogenetic relationships and the true origins of each order in these four lineages. ...
... The A3 locus is specific to mammals, yet there is significant variation in the number and arrangement of individual A3 family members across species (Figure 2) [50]. For instance, primates and rodents are relatives within the superorder of placental mammals, Euarchontoglires [63][64][65]. However, primate and rodent genomes contain dramatically different numbers of A3 genes: seven A3 genes are encoded in primates while only one is encoded in rodents [49,[66][67][68][69]. Additionally, other mammals grouped together within the superorder Laurasiatheria [68] have varying numbers of A3s, including dog/pig (two) [70], sheep/cow (three) [71], cat (four) [70], and horse (six) [72]. ...
The apolipoprotein B messenger RNA-editing, enzyme-catalytic, polypeptide-like 3 (APOBEC3) family of cytidine deaminases plays an important role in the innate immune response to viral infections by editing viral genomes. However, the cytidine deaminase activity of APOBEC3 enzymes also induces somatic mutations in host genomes, which may drive cancer progression. Recent studies of human papillomavirus (HPV) infection and disease outcome highlight this duality. HPV infection is potently inhibited by one family member, APOBEC3A. Expression of APOBEC3A and APOBEC3B is highly elevated by the HPV oncoproteins E6 and E7 during persistent virus infection and disease progression. Furthermore, there is a high prevalence of APOBEC3A and APOBEC3B mutation signatures in HPV-associated cancers. These findings suggest that induction of an APOBEC3-mediated antiviral response during HPV infection may inadvertently contribute to cancer mutagenesis and virus evolution. Here, we discuss current understanding of APOBEC3A and APOBEC3B biology in HPV restriction, evolution, and associated cancer mutagenesis.
... Tout comme les tatous, ils peuvent se rouler en boule en cas de danger (Lecointre & Le Guyader, 2001). Les Carnivora ( Figure 2) constituent un ordre créé par Bowdich en 1821 (Carnivora, 2013). ...
Les relations phylogénétiques des ordres de mammifères n’a pas toujours été la même qu’actuellement et a beaucoup varié au gré des méthodes et des analyses employées. Mon étude a pour objectif d’analyser l’évolution et la pertinence des relations de parenté de deux ordres mammaliens, les Carnivora et les Pholidota, deux taxons aujourd’hui considérés comme groupes-frères dans presque toutes les analyses publiées. Mon travail est fondé sur une analyse bibliographique et le but sera de confronter les résultats moléculaires et morphologiques. Certaines conclusions des auteurs ont été retenues dans ce mémoire, notamment la création du clade des Pholidotamorpha, réunissant Pholidota (pangolins actuels) et Palaeanodonta (pangolins fossiles) ; ainsi que le clade des Ostentoria, regroupant Carnivora et Pholidotamorpha, préféré aux Ferae, pour des raisons épistémologiques. Un consensus actuel a pu en être retenu, mais de nouvelles études devront être effectuées. Pour établir la phylogénie de plusieurs ordres, il est nécessaire d’employer des analyses à la fois moléculaire, en prenant un maximum de données, et morphologiques, en tenant compte des registres fossiles.
... Fig. 2 shows a phylogeny mandala of Eutheria. The phylogenetic relationships are based on Waddell et al. (1999), Murphy et al. (2001), Amrine-Madsen et al. (2003), Nishihara et al. (2006), Matthee et al. (2007), and dos Reis et al. (2012). Branch lengths are approximately proportional to the time-scale estimated by dos Reis et al. (2012), and the red circle indicates 66 Mya (K/Pg Boundary), when dinosaurs became extinct. ...
A circular phylogeny with photos or drawings of species is named a phylogeny mandala. This is one of the ways for illustrating the Tree of Life, and is suitable to show visually how the biodiversity has developed in the course of evolution as clarified by the molecular phylogenetics. To demonstrate the recent progress of molecular phylogenetics, six phylogeny mandalas for various taxonomic groups of life were presented; i.e., (1) Eukaryota, (2) Metazoa, (3) Hexapoda, (4) Tetrapoda, (5) Eutheria, and (6) Primates.
... The three competing hypotheses for the placental root posit basal splits between (i) Exafroplacentalia and Afrotheria, (ii) Xenarthra and Epitheria, and (iii) Atlantogenata and Boreoeutheria (Teeling & Hedges [43]; table 2). Many of the early large-scale molecular phylogenetic studies favoured Afrotheria versus Exafroplacentalia [15,16,[26][27][28]44], but Atlantogenata versus Boreoeutheria and to a lesser extent Xenarthra versus Epitheria also received support, sometimes in the same studies that provided support for Afrotheria versus Exafroplacentalia [15,16,28]. Meredith et al.'s [4] multigene dataset, which expanded gene sampling to 26 loci (totalling approx. ...
Most molecular phylogenetic studies place all placental mammals into four superordinal groups, Laurasiatheria (e.g. dogs, bats, whales), Euarchontoglires (e.g. humans, rodents, colugos), Xenarthra (e.g. armadillos, anteaters) and Afrotheria (e.g. elephants, sea cows, tenrecs), and estimate that these clades last shared a common ancestor 90–110 million years ago. This phylogeny has provided a framework for numerous functional and comparative studies. Despite the high level of congruence among most molecular studies, questions still remain regarding the position and divergence time of the root of placental mammals, and certain ‘hard nodes’ such as the Laurasiatheria polytomy and Paenungulata that seem impossible to resolve. Here, we explore recent consensus and conflict among mammalian phylogenetic studies and explore the reasons for the remaining conflicts. The question of whether the mammal tree of life is or can be ever resolved is also addressed.
This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.
... Placements of non-perissodactyl and non-paenungulate fossil taxa were largely stable across all of these analyses, but relationships of stem and crown perissodactyls were not. Bootstrap support along the perissodactyl stem lineage was consistently ,50%, but it should be noted that support was also ,50% for several clades (e.g., Afroinsectivora, Afrotheria, Paenungulata, Laurasiatheria) that are strongly supported by maximum likelihood and Bayesian analyses of molecular data [27,[95][96][97][98]. Low support values for several nodes are probably due to dense sampling of incomplete fossil taxa that might decrease stability, but preserve intermediate states that break up long branches [99,100]. ...
... The previous lists of species were presented in 1984(Kryhanovsky, Emelianov, 1984 and 1965 (Korneyev, 1965). In the mammals taxonomy ranks higher than family correspond to the review by McKenna and Bell (1997), with some corrections (Wilson, Reeder, 2005;Amrine-Madsen et al., 2003;Asher et al., 2009 etc.). It is important to note that the analysis of fauna changes should be conducted with clear distinction between real changes in fauna composition and subjective changes of researcher's views on fauna composition . ...
The species composition in the mammal fauna of Ukraine for the last three centuries has been analyzed. Estimates of species richness were presented for families, superfamilies, suborders and orders. The data were grouped into superorders: Glires (58 species, 52 of them in the modern fauna), Lipotyphla (14, 12), Chiroptera (29, 28), Ferae (23, 21), Ungulata (22, 18). The modern mammal fauna includes 131 species (among them 23 alien species); in addition, 15 species became extinct during the last 300 years. Thus, the complete list of Ukrainian mammal fauna (including extinct mammals) includes 146 species. There are also 9 “phantom” species which were not included in diversity indices or fauna changes calculations. The index of fauna changes (IFR) is 15.4 %; it has the maximum in Ungulata (42.9 %) and Ferae (23.5 %), and the minimum in Lipotyphla (7.1 %) and Chiroptera (5.6 %). The rates of fauna changes are increasing over time, and they reached the highest values in the last few decades.
... Different arguments (Irwin and Arnason 1994;Philippe and Douzery 1994;Gatesy et al. 1996;Allard et al. 1996;Luckett and Hong 1998) were put forward in support of the view that the hippocetacean relationship was artifactual and resulted from: (i) a nuclear copy obtained for the hippo cytochrome b; (ii) convergent evolution because of similar way of life in water; (iii) homoplasies in the cytochrome b; (iv) lack of representation of all mammal orders. Numerous papers subsequently published try to confirm or invalidate the Hippo-Cetacea association by including more mammalian diversity and more mitochondrial (Milinkovitch et al. 1994;Montgelard et al. 1997;Ursing and Arnason 1998) and/or nuclear markers (pancreatic ribonucleases: Philippe and Douzery 1994;caseins: Gatesy et al. 1996; interphotoreceptor retinoid binding protein [IRBP]: Stanhope et al. 1996;von Willebrand factor [vWF]: Porter et al. 1996;fibrinogen: Gatesy 1997;lactalbumin: Milinkovitch et al. 1998;nuclear introns: Matthee et al. 2001; alpha 2B adrenergic receptor [A2AB]: Madsen et al. 2002;apolipoprotein B [APOB]: Amrine- Madsen et al. 2003) used alone or in combination. All these studies, however, suffered from a lack of taxonomic representativeness and/or informative characters (number and choice of genes) to improve accuracy in the inferred molecular relationships. ...
... Placements of non-perissodactyl and non-paenungulate fossil taxa were largely stable across all of these analyses, but relationships of stem and crown perissodactyls were not. Bootstrap support along the perissodactyl stem lineage was consistently ,50%, but it should be noted that support was also ,50% for several clades (e.g., Afroinsectivora, Afrotheria, Paenungulata, Laurasiatheria) that are strongly supported by maximum likelihood and Bayesian analyses of molecular data [27,[95][96][97][98]. Low support values for several nodes are probably due to dense sampling of incomplete fossil taxa that might decrease stability, but preserve intermediate states that break up long branches [99,100]. ...
... Phylogenetic analyses of the four concatenated genes using maximum likelihood and Bayesian inference provided a robustly supported picture for the 60 assessed mammalian taxa (Fig. 2). This phylogenetic tree showed placental mammal relationships that are fully in line with the four-way division revealed by classical multigene analyses, with strong support obtained for Afrotheria, Xenarthra, Euarchontoglires, Laurasiatheria, and Boreoeutheria (Amrine- Madsen et al., 2003;Delsuc et al., 2002;Murphy et al., 2001;Springer et al., 2007). Most other placental inter-ordinal relationships were also strongly supported, with the notable exceptions of the position of the root and the relationships among Laurasiatherian orders, where ancient incomplete lineage sorting events probably obscured the phylogenetic signal (Churakov et al., 2009;Murphy et al., 2007;Nishihara et al., 2009;Prasad et al., 2008). ...
Fairy armadillos or pichiciegos (Xenarthra, Dasypodidae) are among the most elusive mammals. Due to their subterranean and nocturnal lifestyle, their basic biology and evolutionary history remain virtually unknown. Two distinct species with allopatric distributions are recognized: Chlamyphorus truncatus is restricted to central Argentina, while Calyptophractus retusus occurs in the Gran Chaco of Argentina, Par-aguay, and Bolivia. To test their monophyly and resolve their phylogenetic affinities within armadillos, we obtained sequence data from modern and museum specimens for two mitochondrial genes (12S RNA [MT-RNR1] and NADH dehydrogenase 1 [MT-ND1]) and two nuclear exons (breast cancer 1 early onset exon 11 [BRCA1] and von Willebrand factor exon 28 [VWF]). Phylogenetic analyses provided a reference phylogeny and timescale for living xenarthran genera. Our results reveal monophyletic pichici-egos as members of a major armadillo subfamily (Chlamyphorinae). Their strictly fossorial lifestyle probably evolved as a response to the Oligocene aridification that occurred in South America after their divergence from Tolypeutinae around 32 million years ago (Mya). The ancient divergence date (17 Mya) for separation between the two species supports their taxonomic classification into distinct genera. The synchronicity with Middle Miocene marine incursions along the Paraná river basin suggests a vicariant origin for pichiciegos by the disruption of their ancestral range. Their phylogenetic distinctiveness and rarity in the wild argue in favor of high conservation priority.
... To further explore the potential impact of selected variants on protein function, we chose three high-ranking genes, APOB, LIPG and USH2A, for which protein domain structure and other relevant literature were readily available. For APOB, which is one of the most complex proteins in the genome with regard to exon structure, we focused on exon 26, which encodes the most important functional domains (Young 1990;Amrine-Madsen et al. 2003). Three missense mutations within APOB occurred in a region from AA 1425 to AA 1728 in humans (AA 1563 to AA 1866 in wolves) (Fig. S16A, Supporting information) which is crucial for forming triglyceride-rich LDL particles (Young 1990) and is a conserved outer membrane channel domain (NCBI c121487). ...
In an era of ever-increasing amounts of whole genome sequence data for individuals and populations, the utility of traditional single nucleotide polymorphisms (SNPs) array-based genome scans is uncertain. We previously performed a SNP array-based genome scan to identify candidate genes under selection in six distinct gray wolf (Canis lupus) ecotypes. Using this information, we designed a targeted capture array for 1040 genes, including all exons and flanking regions, as well as 5000 1 kb non-genic neutral regions and resequenced these regions in 107 wolves. Selection tests revealed striking patterns of variation within candidate genes relative to non-candidate regions and identified potentially functional variants related to local adaptation. We found 27% and 47% of candidate genes from the previous SNP array study had functional changes that were outliers in SweeD and Bayenv analyses, respectively. This result verifies the use of genome wide SNP surveys to tag genes that contain functional variants between populations. We highlight non-synonymous variants in APOB, LIPG, and USH2A that occur in functional domains of these proteins, and that demonstrate high correlation with precipitation seasonality and vegetation. We find Arctic and High Arctic wolf ecotypes have higher numbers of genes under selection, which highlight their conservation value and heightened threat due to climate change. This study demonstrates that combining genome wide genotyping arrays with large scale resequencing and environmental data provides a powerful approach to discern candidate functional variants in natural populations. This article is protected by copyright. All rights reserved.
... The seminal molecular phylogenetic studies of placentals have shown convincingly that armadillos, anteaters, and sloths (Xenarthra) constitute one of the four major placental clades, establishing them as an essential component of the early placental radiation alongside Afrotheria, Laurasiatheria, and Euarchontoglires Murphy, Eizirik, Johnson, et al. 2001;). Yet, despite studies using multigene data (Delsuc et al. 2002;Amrine-Madsen et al. 2003;Meredith et al. 2011), retroposon insertions (Churakov et al. 2009;Nishihara et al. 2009) and genome-wide data (McCormack et al. 2012;Song et al. 2012;Romiguier et al. 2013), their exact position within placentals remains contentious. ...
Xenarthra (armadillos, sloths, and anteaters) constitutes one of the four major clades of placental mammals. Despite their phylogenetic distinctiveness in mammals, a reference phylogeny is still lacking for the 31 described species. Here we used Illumina shotgun sequencing to assemble 33 new complete mitochondrial genomes, establishing Xenarthra as the first major placental clade to be fully sequenced at the species level for mitogenomes. The resulting data set allowed the reconstruction of a robust phylogenetic framework and timescale that are consistent with previous studies conducted at the genus level using nuclear genes. Incorporating the full species diversity of extant xenarthrans points to a number of inconsistencies in xenarthran systematics and species definition. We propose to split armadillos in two distinct families Dasypodidae (dasypodines) and Chlamyphoridae (euphractines, chlamyphorines, and tolypeutines) to better reflect their ancient divergence, estimated around 42 million years ago. Species delimitation within long-nosed armadillos (genus Dasypus) appeared more complex than anticipated, with the discovery of a divergent lineage in French Guiana. Diversification analyses showed Xenarthra to be an ancient clade with a constant diversification rate through time with a species turnover driven by high but constant extinction. We also detected a significant negative correlation between speciation rate and past temperature fluctuations with an increase in speciation rate corresponding to the general cooling observed during the last 15 million years. Biogeographic reconstructions identified the tropical rainforest biome of Amazonia and the Guiana Shield as the cradle of xenarthran evolutionary history with subsequent dispersions into more open and dry habitats.
Phylogenetic studies have resolved most relationships among Eutherian Orders. However, the branching order of elephants ( Proboscidea ), hyraxes ( Hyracoidea ), and sea cows ( Sirenia ) (i.e., the Paenungulata ) has remained uncertain since at least 1758, when Linnaeus grouped elephants and manatees into a single Order ( Bruta ) to the exclusion of hyraxes. Subsequent morphological, molecular, and large-scale phylogenomic datasets have reached conflicting conclusions on the branching order within Paenungulates . We use a phylogenomic dataset of alignments from 13,388 protein-coding genes across 261 Eutherian mammals to infer phylogenetic relationships within Paenungulates . We find that gene trees almost equally support the three alternative resolutions of Paenungulate relationships and that despite strong support for a Proboscidea + Hyracoidea split in the multispecies coalescent (MSC) tree, there is significant evidence for gene tree uncertainty, incomplete lineage sorting, and introgression among Proboscidea , Hyracoidea , and Sirenia . Indeed, only 8-10% of genes have statistically significant phylogenetic signal to reject the hypothesis of a Paenungulate polytomy. These data indicate little support for any resolution for the branching order Proboscidea , Hyracoidea , and Sirenia within Paenungulata and suggest that Paenungulata may be as close to a real, or at least unresolvable, polytomy as possible.
The extraordinary morphological diversity among extant mammals poses a challenge for studies of speciation, adaptation, molecular evolution, and reproductive isolation. Despite the recent wealth of molecular studies on mammalian phylogenetics, uncertainties remain surrounding both ancestral and more recent divergence events that have proven difficult to resolve. Multi-gene datasets, especially including genes that are highly divergent, often provide increased support for higher-level affinities within Mammalia; however, such analyses require vast amounts of genomic sequence data and at times, intensive, high-performance computational effort. Furthermore, despite the large-scale efforts dedicated to comprehensive, multi-gene phylogenetic analyses using a combination of mitochondrial, nuclear, and other sequences (e.g., tRNA, ultra-conserved elements, and transposable elements), many relationships across Mammalia remain highly controversial. To offer another approach and provide a phylogenetic solution to this longstanding issue, here we present a phylogenetic tool based on a single reproductive molecular marker, zonadhesin (gene: Zan), one of two known mammalian speciation genes, which encodes the rapidly evolving sperm protein zonadhesin that mediates species-specific adhesion to the egg and thereby promotes reproductive isolation among placental mammals (Eutheria). Topological comparison of Zan Maximum Likelihood phylogenies to a nearly complete mammalian supertree confirmed Zan’s striking phylogenetic utility and resolution at both deeper and more terminal nodes in the placental mammalian phylogeny. This single gene marker yields an equivalent and/or superiorly supported topology in comparison to a supertree generated using DNA sequences from a supermatrix of 31 genes from 5911 species (extinct and extant). Resolution achieved with this new phylogenetic approach provides unique insights into the divergence of both early and recent mammalian radiations. Finally, and perhaps most importantly, the utility of zonadhesin as a singular molecular marker was especially useful in clades where sufficient taxon sampling is impossible to achieve, and where only a subset of members of the mammalian species tree is available. The eutherian relationships presented here provide a foundation for future studies in the reconstruction of mammalian classifications, including reproductive isolation, hybridization, and biodiversification of species.
The IL‐6 family of cytokines, known for their pleiotropic behavior, share binding to the gp130 receptor for signal transduction with the necessity to bind other receptors. Leukemia inhibitory factor receptor is triggered by the IL‐6 family proteins: leukemia inhibitory factor (LIF), oncostatin‐M (OSM), cardiotrophin‐1 (CT‐1), ciliary neurotrophic factor (CNTF), and cardiotrophin‐like cytokine factor 1 (CLCF1). Besides the conserved binding sites to the receptor, not much is known in terms of the diversity and characteristics of these proteins in different organisms. Herein, we describe the sequence analysis of LIF, OSM, and CT‐1 from several organisms, and m17, a LIF ortholog found in fishes, regarding its phylogenetics, intrinsic properties, and the impact of conserved residues on structural features. Sequences were identified in seven classes of vertebrates, showing high conservation values in binding site III, but protein‐dependent results on binding site II. GRAVY, isoelectric point, and molecular weight parameters were relevant to differentiate classes in each protein and to enable, for the first time and with high fidelity, the prediction of both organism class and protein type just using machine learning approaches. OSM sequences from primates showed an increased BC loop when compared to the remaining mammals, which could influence binding to OSM receptor and tune signaling pathways. Overall, this study highlights the potential of sequence diversity analysis to understand IL‐6 cytokine family evolution, showing the conservation of function‐related motifs and evolution of class and protein‐dependent characteristics. Our results could impact future medical treatment of disorders associated with imbalances in these cytokines.
The current literature on marsupial phylogenetics includes numerous studies based on analyses of morphological data with limited sampling of Recent and fossil taxa, and many studies based on analyses of molecular data with dense sampling of Recent taxa, but few studies have combined both data types. Another dichotomy in the marsupial phylogenetic literature is between studies focused on New World taxa and those focused on Sahulian taxa. To date, there has been no attempt to assess the phylogenetic relationships of the global marsupial fauna based on combined analyses of morphology and molecular sequences for a dense sampling of Recent and fossil taxa. For this report, we compiled morphological and molecular data from an unprecedented number of Recent and fossil marsupials. Our morphological data consist of 180 craniodental characters that we scored for 97 terminals representing every currently recognized Recent genus, 42 additional ingroup (crown-clade marsupial) terminals represented by well-preserved fossils, and 5 outgroups (nonmarsupial metatherians). Our molecular data comprise 24.5 kb of DNA sequences from whole-mitochondrial genomes and six nuclear loci (APOB, BRCA1, GHR, RAG1, RBP3 and VWF) for 97 marsupial terminals (the same Recent taxa scored for craniodental morphology) and several placental and monotreme outgroups. The results of separate and combined analyses of these data using a wide range of phylogenetic methods support many currently accepted hypotheses of ingroup (marsupial) relationships, but they also underscore the difficulty of placing fossils with key missing data (e.g., Evolestes), and the unique difficulty of placing others that exhibit mosaics of plesiomorphic and autapomorphic traits (e.g., Yalkaparidon). Unique contributions of our study are (1) critical discussions and illustrations of marsupial craniodental morphology including features never previously coded for phylogenetic analysis; (2) critical assessments of relative support for many suprageneric clades; (3) estimates of divergence times derived from tip-and-node dating based on uniquely taxon-dense analyses; and (4) a revised, higher-order classification of marsupials accompanied by lists of supporting craniodental synapomorphies. Far from the last word on these topics, this report lays the foundation for future research that may be enabled by the discovery of new fossil taxa, better-preserved material of previously described taxa, novel morphological characters (e.g., from the postcranium), and improved methods of phylogenetic analysis.
Resolving the interordinal relationships in the mammalian superorder Laurasiatheria has been among the most intractable problems in higher-level mammalian systematics, with many conflicting hypotheses having been proposed. The present study collected three different sources of genome-scale data with comprehensive taxon sampling of laurasiatherian species, including two protein-coding datasets (4,186 protein-coding genes for an amino acid dataset comprising 2,761,247 amino acid residues and a nucleotide dataset comprising 5,516,340 nucleotides from 1st and 2nd codon positions), an intronic dataset (1,210 introns comprising 1,162,723 nucleotides) and an ultraconserved elements (UCEs) dataset (1,246 UCEs comprising 1,946,472 nucleotides) from 40 species representing all six laurasiatherian orders and 7 non-laurasiatherian outgroups. Remarkably, phylogenetic trees reconstructed with the four datasets using different tree-building methods (RAxML, FastTree, ASTRAL and MP-EST) all supported the relationship (Eulipotyphla, (Chiroptera, ((Carnivora, Pholidota), (Cetartiodactyla, Perissodactyla)))). We find a resolution of interordinal relationships of Laurasiatheria among all types of markers used in the present study, and the likelihood ratio tests for tree comparisons confirmed that the present tree topology is the optimal hypothesis compared to other examined hypotheses. Jackknifing subsampling analyses demonstrate that the results of laurasiatherian tree reconstruction varied with the number of loci and ordinal representatives used, which are likely the two main contributors to phylogenetic disagreements of Laurasiatheria seen in previous studies. Our study provides significant insight into laurasiatherian evolution, and moreover, an important methodological strategy and reference for resolving phylogenies of adaptive radiation, which have been a long-standing challenge in the field of phylogenetics.
Isolated astragali and calcanei of one of the smallest known living or extinct mammals, the geolabidid lipotyphlan Batodonoides powayensis, are identified and described from early and late Uintan (middle Eocene) strata in San Diego County, California. The morphology of the tarsus of Batodonoides appears to be most consistent with arboreal or scansorial locomotion. Prior assessments of geolabidid relationships have allied the group with lipotyphlans, particularly soricids and Solenodon, but the tarsus of Batodonoides shows no particular similarity to any extant lipotyphlan family. Instead, there are unexpected tarsal similarities to the extinct Nyctitheriidae, suggesting that geolabidids may have their origins among Paleocene and Eocene nyctitheres. Results of a phylogenetic analysis are consistent with a relationship either to Solenodon or to Nyctitheriidae. When geolabidids and nyctitheres are allied, the latter group shifts from the euarchontan stem to the lipotyphlan stem, potentially reconciling two divergent views on the relationships of nyctitheres. Batodonoides provides an additional example of the impact of nondental material in challenging established views of the affinities of early Cenozoic ‘insectivores.’
We report a new genus and species of herbivorous mammal, Pahelia mysteriosa, from the early Eocene Cambay Shale Formation, Tadkeshwar Lignite Mine, Gujarat, India. The new taxon, approximately the size of a small phenacodontid (e.g. Ectocion parvus), is represented by three mandibular fragments, the most complete of which documents nearly the entire symphysis and mandibular body plus P3–M3. Pahelia has incipiently selenolophodont molars with strong exodaenodonty, absent paraconids, weak but distinct entolophids, and prominent ectostylids. Molar size increases distally, but M3 does not develop a prominent third lobe. Premolars are simple, with prominent protoconids and short talonids but little development of other trigonid cusps. The mandibular symphysis is strongly fused, and there is an enlarged alveolus for an anterior tooth. The combination of features present in the new taxon does not closely match that of any known mammal, but there are some similarities to a diversity of ungulates from Africa, Asia, Europe and North America. Preserved morphology is insufficient to assess the affinities of the new taxon with confidence, but a link to Quettacyonidae, also endemic to the Indian subcontinent, is morphologically and biogeographically plausible. If this scenario is correct, it suggests that P. mysteriosa could be a part of the endemic mammalian fauna of India prior to its initial faunal contact with Asia.
An edentulous partial skeleton of a carnivorous mammal from the Uinta Formation (middle Eocene) of Utah is referred to the rare and enigmatic sabre-tooth clade Machaeroidinae primarily on the basis of alveolar patterns and cranial morphology. The newly recognized skeleton includes portions of both girdles, all long bones, and the first known tarsal and phalangeal material of a machaeroidine. The specimen permits a preliminary reconstruction of the locomotor habits of machaeroidines, which appear to have been adapted to scansorial or arboreal rather than terrestrial locomotion. The new material also prompts a review of machaeroidine affinities, which have been unresolved for over a century, with consensus opinion favouring a link to either oxyaenid or limnocyonine hyaenodontid ‘creodonts’. Postcranial evidence favours a link to oxyaenids, as machaeroidines share numerous features with oxyaenids that are lacking in hyaenodontids. To test this relationship machaeroidines were included in a phylogenetic analysis broadly sampling early carnivorous eutherians, including members of both ‘Creodonta’ and Carnivoramorpha. Results place Machaeroidinae within Oxyaenidae but fail to support either ‘creodont’ or carnivoramorphan monophyly. Instead, Oxyaenidae is linked with Carnivoraformes, while Viverravidae is basally positioned among carnivorous eutherians. Reconsideration of the character evidence cited in support of Carnivoramorpha indicates that many features are ambiguous in the context of a broad sample of ‘creodonts’ and early carnivoramorphans. Hyaenodontid monophyly is also not recovered but this likely reflects the influence of one morphologically divergent genus, Arfia.
Temminck's ground pangolin is the only pangolin present in South Africa. It is a myrmecophagous mammal with a bipedal gait. The thoracic limbs are used to break open ant nests, dig for food and expand previously occupied burrows. This study describes the osteology and radiological anatomy of the thoracic limbs of this threatened species. Thoracic limbs from four Temminck's ground pangolins, which succumbed from electrocution or natural causes, were digitally radiographed in situ. The individual bones were then cleaned, described and digitally radiographed. The skeleton of the thoracic limbs revealed a similar number and arrangement of bones compared to that of domestic carnivores. The bones were robust and displayed numerous open epiphyseal lines. The latter provide an estimate of sexual maturity and should not be confused with fractures in injured ground pangolins. The scapula was broad and triangular-shaped. The humerus displayed a massive medial epicondyle. The radius and ulna were similarly sized, and displayed a broad radial trochlea and large olecranon tuber, respectively. The manus was composed of seven carpal bones, five short metacarpal bones and five digits of which the three central digits were the best developed. The unguicular process of the distal phalanx was bifid and elongated. The osteological characteristics indicate that the thoracic limbs of Temminck's ground pangolin are specifically adapted for protraction and retraction, strong elbow extension, flexion of the carpus and digits as well as pronation and supination of the antebrachium, as opposed to weight-bearing. These functions are likewise documented for other scratch-digging species. This article is protected by copyright. All rights reserved.
Phylogenetics aims to study the evolutionary relatedness of living organisms in our planet. Its application is extended to the key areas such as evolution, classification and taxonomy of living organisms; ecology, diversity, and conservation biology of agrobiocenosis; monitoring of pathogen spread, outbreaks and source of transmissions, forensic analyses, etc. Historically, phylogenetics studies were prevalently based on morphological features of species that helped to classify the 'Tree of Life' on Earth. Modern phylogenetics studies, however, rely more heavily on DNA sequences. In this Phylogenetics book, we aimed to present readers the latest developments in phylogenetics studies that highlight multi-kingdom systems, reticulated evolution and conservation biology of living organisms as well as 'omics'-based phylogenetics advances.
Freely available at: https://www.intechopen.com/books/phylogenetics
The maned sloth Bradypus torquatus (Bradypodidae:Pilosa) is an endangered and endemic species of the Atlantic Forest in Brazil, a biome that was anthropogenically reduced to about 7% of its original extent. Nowadays, an apparently decreasing population is restricted to few remaining rainforest fragments. We analyzed nuclear and mitochondrial genes of 69 individuals from the Brazilian states of Bahia, Espírito Santo and Rio de Janeiro to estimate their current and historical population dynamics. The diversification history of B. torquatus populations was mainly led by dispersal and vicariant events occurring during Pliocene and Pleistocene associated to several climatic and vegetation changes. Besides, the current distribution of remaining populations was also likely affected by recent anthropogenic deforestation occurring in the last five centuries in Brazil, resulting in local extinction of many intermediate B. torquatus populations. Our time scaled phylogeographic results indicate that in the Pliocene, an ancestral population of B. torquatus was originally located in the intermediate Atlantic Forest region between BA and ES states and dispersed northwards and southwards to its current range. These results indicate also that the northern and southern Atlantic Forest B. torquatus lineages should have independent management plans and conservation policies due to their ancient history of isolation and evolutionary independency.
The widespread use of mouse models in developmental, behavioural and genetic studies has sparked wider interest in rodent biology as a whole. This book brings together the latest research on rodents to better understand the evolution of both living and extinct members of this fascinating group. Topics analysed include the role of molecular techniques in the determination of robust phylogenetic frameworks; how geometric morphometric methods help quantify and analyse variation in shape; and the role of developmental biology in elucidating the origins of skeletal elements and the teeth. The editors unite these disciplines to present the current state of knowledge in rodent biology, whilst setting the landscape for future research. This book highlights interdisciplinary links across palaeontology, developmental biology, functional morphology, phylogenetics and biomechanics, making it a valuable resource for evolutionary biologists in all fields.
The widespread use of mouse models in developmental, behavioural and genetic studies has sparked wider interest in rodent biology as a whole. This book brings together the latest research on rodents to better understand the evolution of both living and extinct members of this fascinating group. Topics analysed include the role of molecular techniques in the determination of robust phylogenetic frameworks; how geometric morphometric methods help quantify and analyse variation in shape; and the role of developmental biology in elucidating the origins of skeletal elements and the teeth. The editors unite these disciplines to present the current state of knowledge in rodent biology, whilst setting the landscape for future research. This book highlights interdisciplinary links across palaeontology, developmental biology, functional morphology, phylogenetics and biomechanics, making it a valuable resource for evolutionary biologists in all fields.
The widespread use of mouse models in developmental, behavioural and genetic studies has sparked wider interest in rodent biology as a whole. This book brings together the latest research on rodents to better understand the evolution of both living and extinct members of this fascinating group. Topics analysed include the role of molecular techniques in the determination of robust phylogenetic frameworks; how geometric morphometric methods help quantify and analyse variation in shape; and the role of developmental biology in elucidating the origins of skeletal elements and the teeth. The editors unite these disciplines to present the current state of knowledge in rodent biology, whilst setting the landscape for future research. This book highlights interdisciplinary links across palaeontology, developmental biology, functional morphology, phylogenetics and biomechanics, making it a valuable resource for evolutionary biologists in all fields.
Ground squirrels of the genus Marmota are known for their ability to tolerate bitterly cold climates, which they in part accomplish with their exceptional ability to hibernate for as much as eight months a year (Armitage et al., 2003). Most of the 15 living species are associated with montane habitats, and those that are not, like the North American woodchuck (Marmota monax) and the eastern European and central Asian bobak (M. bobak) inhabit regions with strongly seasonal climates and often bitterly cold winters (Armitage, 2000) (Figure 9.1). All marmots construct burrows, which can be more than one metre deep even in comparatively mild climates and as much as seven metres deep in the harsh climates of the Himalayas (Barash, 1989). During the cold phases of the last half of the Quaternary the fossil record demonstrates many marmots inhabited periglacial environments (Zimina and Gerasimov, 1973; Kalthoff, 1999). For these reasons, marmots are sometimes considered to be a quintessentially Quaternary clade, specialists on the cold variable climates that are unique to the past 2.6 million years of Earth’s history. The world in which they originated, however, was very different; a warmer one in which there were no tundra biomes, no glacial-interglacial cycles, and no permanent ice cover in the Northern Hemisphere. In this chapter, we review the fossil and phylogenetic history of marmots, the palaeoenvironments in which they originated, and their relationship to glacial-interglacial cycles to better understand the contexts in which the specializations of this unique clade of rodents arose. The Quaternary, the current geological period, is defined by the onset of permanent ice sheets in the Northern Hemisphere 2.58 million years ago and is by far the coldest period since the extinction of the last non-avian dinosaurs 65 million years ago (Zachos et al., 2001; Gibbard et al., 2010).
The widespread use of mouse models in developmental, behavioural and genetic studies has sparked wider interest in rodent biology as a whole. This book brings together the latest research on rodents to better understand the evolution of both living and extinct members of this fascinating group. Topics analysed include the role of molecular techniques in the determination of robust phylogenetic frameworks; how geometric morphometric methods help quantify and analyse variation in shape; and the role of developmental biology in elucidating the origins of skeletal elements and the teeth. The editors unite these disciplines to present the current state of knowledge in rodent biology, whilst setting the landscape for future research. This book highlights interdisciplinary links across palaeontology, developmental biology, functional morphology, phylogenetics and biomechanics, making it a valuable resource for evolutionary biologists in all fields.
The widespread use of mouse models in developmental, behavioural and genetic studies has sparked wider interest in rodent biology as a whole. This book brings together the latest research on rodents to better understand the evolution of both living and extinct members of this fascinating group. Topics analysed include the role of molecular techniques in the determination of robust phylogenetic frameworks; how geometric morphometric methods help quantify and analyse variation in shape; and the role of developmental biology in elucidating the origins of skeletal elements and the teeth. The editors unite these disciplines to present the current state of knowledge in rodent biology, whilst setting the landscape for future research. This book highlights interdisciplinary links across palaeontology, developmental biology, functional morphology, phylogenetics and biomechanics, making it a valuable resource for evolutionary biologists in all fields.
The early Paleocene diversity of metatherians in Tiupampan faunas of South America and the pre-Tiupampan Paleocene polydolopimorphian Cocatherium speak in favor of an earliest Paleocene or Late Cretaceous dispersal of metatherians from North America. No Late Cretaceous metatherian or eutherian mammals have been recovered to date in South America, but the late Campanian to Maastrichtian hadrosaurine dinosaurs in Argentina, as well as the late Maastrichtian of the Antarctic Peninsula, is evidence of a biotic connection to North America. Placental ‘condylarths’ in the Tiupampan may have been related to, and dispersed southward relative to, Puercan taxa in North America and perhaps reflect a somewhat later event in comparison to metatherians. Other than hadrosaurine dinosaurs, Late Cretaceous vertebrates of South America are basically Gondwanan in affinities and reflect (and survived) the pre-106 Ma connection between South America, Africa, and Antarctica. The potential for a Late Cretaceous dispersal of metatherians would be compatible with a continued dispersal to Australia at that time, also supported by plate tectonic relationships, notwithstanding the basically endemic coeval Australian dinosaur fauna, and recognizing the essential absence of a Late Maastrichtian land vertebrate record there. An early Paleocene connection between at least Antarctica and South America is documented by the presence of a monotreme in the Peligran fauna of Patagonia. This, coupled with the fact that post-Peligran mammal faunas in South America and the Antarctic Peninsula (from at least 52 Ma in that location) are composed of derived metatherian as well as placental mammals, suggests that dispersal of metatherians to Australia had been achieved prior to the Eocene. Such timing is compatible with the still plesiomorphic level of Australian metatherians from the early Eocene Tingamarra fauna of Australia, the marine sundering of the Tasman Gate at about 50 Ma and the development of a continuously marine southern coastline of Australia from about 45 Ma effectively foreclosed overland mammal and other vertebrate dispersal to Australia thereafter.
Vision is the dominant sense in primates. This article attempts to reconstruct a reasonable scenario as to how parallel visual pathways might have evolved in primates by comparing key factors that might distinguish this group evolutionarily. The focus is on visual information channels from the eye through the lateral geniculate nucleus (LGN) of the thalamus to cortex since these pathways may have become uniquely specialized in primate evolution. We defend the position that magnocellular (M) and parvocellular (P) retinogeniculocortical pathways are homologous across primates and therefore probably existed in the mammalian common ancestor of primates. Whether homologues to these visual pathways can be found in extant mammals remains controversial, but evidence suggests that functionally similar pathways can be identified in a range of mammals. Even for the less well-researched koniocellular (K) pathway, data exist suggesting an early evolutionary history. Only among primates, however, is the evidence strong enough to support homology. We also present data suggesting that the common ancestor to primates was dichromatic and that early primates may even have been diurnal given the existence of genes for at least two cone types in all primates. We also review evidence for homologies between ocular dominance pathways and other properties. In addition, we review evidence for the evolutionary history of cortical hierarchies of visual areas and conclude that only a few areas can be considered homologous across primates and even fewer across mammals. In the final section, we provide a summary and also outline questions that should be addressed in order to arrive at more definitive conclusions concerning the evolution of parallel visual pathways. We also outline some practical strategies for answering some of these questions.
The widespread use of mouse models in developmental, behavioural and genetic studies has sparked wider interest in rodent biology as a whole. This book brings together the latest research on rodents to better understand the evolution of both living and extinct members of this fascinating group. Topics analysed include the role of molecular techniques in the determination of robust phylogenetic frameworks; how geometric morphometric methods help quantify and analyse variation in shape; and the role of developmental biology in elucidating the origins of skeletal elements and the teeth. The editors unite these disciplines to present the current state of knowledge in rodent biology, whilst setting the landscape for future research. This book highlights interdisciplinary links across palaeontology, developmental biology, functional morphology, phylogenetics and biomechanics, making it a valuable resource for evolutionary biologists in all fields.
The mammalian order Xenarthra (armadillos, anteaters and sloths) is one of the four major clades of placentals, but it remains poorly studied from the molecular phylogenetics perspective. We present here a study encompassing most of the order's diversity in order to establish xenarthrans' intra-ordinal relationships, discuss the evolution of their morphological characters, search for their extant sister group and specify the timing of their radiation with special emphasis on the status of the controversial fossil Eurotamandua. Sequences of three genes (nuclear exon 28 of the Von Willebrand factor and mitochondrial 12S and 16S rRNAs) are compared for eight of the 13 living genera. Phylogenetic analyses confirm the order's monophyly and that of its three major lineages: armadillos (Cingulata), anteaters (Vermilingua) and sloths ('Tardigrada', renamed in 'Folivora'), and our results strongly support the grouping of hairy xenarthrans (anteaters and sloths) into Pilosa. Within placentals, Afrotheria might be the first lineage to branch off, followed by Xenarthra. The morphological adaptative convergence between New World xenarthrans and Old World pangolins is confirmed. Molecular datings place the early emergence of armadillos around the Cretaceous/Tertiary boundary, followed by the divergence between anteaters and sloths in the Early Eocene era. These Tertiary dates contradict the concept of a very ancient origin of modern xenarthran lineages. They also question the placement of the purported fossil anteater (Eurotamandua) from the Middle Eocene period of Europe with the Vermilingua and instead suggest the independent and convergent evolution of this enigmatic taxon.
We explore the tree of mammalian mtDNA sequences, using particularly the LogDet transform on amino acid sequences, the distance
Hadamard transform, and the Closest Tree selection criterion. The amino acid composition of different species show significant
differences, even within mammals. After compensating for these differences, nearest-neighbor bootstrap results suggest that
the tree is locally stable, though a few groups show slightly greater rearrangements when a large proportion of the constant
sites are removed. Many parts of the trees we obtain agree with those on published protein ML trees. Interesting results include
a preference for rodent monophyly. The detection of a few alternative signals to those on the optimal tree were obtained using
the distance Hadamard transform (with results expressed as a Lento plot). One rearrangement suggested was the interchange
of the position of primates and rodents on the optimal tree. The basic stability of the tree, combined with two calibration
points (whale/cow and horse/rhinoceros), together with a distant secondary calibration from the mammal/bird divergence, allows
inferences of the times of divergence of putative clades. Allowing for sampling variances due to finite sequence length, most
major divergences amongst lineages leading to modern orders, appear to occur well before the Cretaceous/Tertiary (K/T) boundary.
Implications arising from these early divergences are discussed, particularly the possibility of competition between the small
dinosaurs and the new mammal clades.
Recent fossil discoveries have greatly increased our knowledge of the morphology and diversity of early Anthropoidea, the suborder to which humans belong. Phylogenetic analysis of Recent and fossil taxa supports the hypotheses that a haplorhine-strepsir-rhine dichotomy existed at least at the time of the earliest record of fossil primates (earliest Eocene) and that eosimiids (middle Eocene, China) are primitive anthropoids. Functional analysis suggests that stem haplorhines were small, nocturnal, arboreal, visually oriented insectivore-frugivores with a scurrying-leaping locomotion. A change from nocturnality to diurnality was the fundamental adaptive shift that occurred at the base of the tarsier-eosimiid-anthropoid clade. Stem anthropoids remained small diurnal arborealists but adopted locomotor patterns with more arboreal quadrupedalism and less leaping. A shift to a more herbivorous diet occurred in several anthropoid lineages.
For more than a century, systematists have debated higher-level relationships among the orders of placental mammals. The order Primates is noexception. One prominent hypothesis is Archonta that was originally proposed as a superorder by Gregory (1910) to include primates, bats, flying lemurs, and menotyphlan insectivores (i.e., tree shrews, elephant shrews). Minus elephant shrews, the Archonta hypothesis has survived for nearly a century. The bulk of support for this hypothesis derives from modifications of the tarsus (Novacek and Wyss, 1986; Shoshani and McKenna, 1998; Szalay, 1977; Szalay and Drawhorn, 1980; Szalay and Lucas, 1993). Archonta is a recurrent theme in higher-level mammalian classifications (McKenna, 1975; McKenna and Bell, 1997; Szalay, 1977). There are also morphological studies (Cartmill and MacPhee, 1980; Luckett, 1980; Novacek, 1980; Simpson, 1945) that question the monophyly of Archonta. Simpson (1945) suggested that Archonta is "almost surely an unnatural group." Even among studies that advocate Archonta, the possibility that bats are an independently arboreal group from the Archonta has been noted (Szalay and Drawhorn, 1980). In part, this reservation was expressed because bats lack shared, derived tarsal specializations that unite other archontans (Szalay, 1977; Szalay and Drawhorn, 1980). Szalay and Drawhorn (1980) attribute this to the major functional transformation that the chiropteran ankle has undergone in association with the "extreme reorientation of the femoral-acetabular articulation." Given the absence of tarsal modifications that unite bats with other archontans, the primary rationale for including bats in Archonta is the suite of novel features that bats share with flying lemurs (Gregory, 1910; Simmons, 1995; Simmons and Quinn, 1994; Szalay and Drawhorn, 1980). Aside from whether or not primates belong to a monophyletic Archonta, there are questions pertaining to the sister-group of primates. Several studies resolve archontans into a trichotomy between primates, tree shrews, and Volitantia (i.e., flying lemurs bats) (Novacek, 1990; Novacek et al., 1988; Novacek and Wyss, 1986; Szalay, 1977). Other studies, some of which support Archonta and others of which do not, support a sister-group relationship between primates (or euprimates) and tree shrews (Martin, 1990; Shoshani and McKenna, 1998; Simpson, 1945; Wible and Covert, 1987; Wible and Novacek, 1988). Beard (1993) has argued for the Primatomorpha hypothesis that postulates a sister-group relationship between flying lemurs and primates. Another alternative is a sister-group relationship between tree shrews and flying lemurs, with this collective group as the sister-group to primates (Sargis, 2001).
A suite of comparisons among ten radiolabelled dasyurid species and one outgroup bandicoot was generated using the hydroxyapatite chromatography method of DNA-DNA hybridisation; comparisons were also made with four other dasyurid taxa. Square matrices of DELTA-T(m)s, DELTA-Modes, and DELTA-T50H's were complied and corrected for reciprocity, additivity, and, in the case of DELTA-T(m)'s, normalised percentages of hybridisation. These matrices were analysed using the FITCH algorithm in Felsenstein's PHYLIP (Version 3.1), and all distinct topologies were jackknifed to test for internal consistency. Additionally, uncorrected DELTA-T(m), DELTA-Mode, and DELTA-T50H datasets were bootstrapped and subjected to phylogenetic analysis to assess measurement imprecision. FITCH trees from folded matrices including unlabelled species or those for which heteroduplex comparisons were incomplete were also calculated and jack-knifed, both before and after correction. With the exception of limited measurements to Dasyuroides byrnei and Dasykaluta rosamondae, which showed affinities with Dasyurus spp., the final tree was fully resolved: Sminthopsis crassicaudata and S. murina, together with the more distant Planigale maculata, are the sister-group to all other dasyurids examined, which in turn comprise two clades. One of these includes Dasyurus, Dasyuroides, and Dasykaluta; the other, 'true' Antechinus (A. flavipes, A. stuartii, A. swainsonii) as a sister-group to Antechinus melanurus plus Murexia longicaudata, with Phascogale tapoatafa representing a probable sister-group to all Antechinus with Murexia. DNA-DNA hybridisation provides no support for the genus Satanellus: most of the trees linked Dasyurus albopunctatus with D. maculatus instead of D. hallucatus. Similarly, Antechinus flavipes and A. stuartii appear to be closer to each other than either is to A. swainsonii. The historical biogeographic significance of the adopted phylogeny is considered, and it is concluded that the putative early Miocene separation of Australia and New Guinea was probably too early to account for the independent evolution of the New Guinean clade.
Several novel (sub)families of SINEs were isolated from the genomes of cetaceans and artiodactyls, and their sequences were determined. From comparisons of diagnostic nucleotides among the short interspersed repetitive elements (SINEs) in these (sub)families, we were able to draw the following conclusions. (1) After the divergence of the suborder Tylopoda (camels), the CHRS family of SINEs was newly created from tRNA Glu in a common ancestor of the lineages of the Suina (pigs and peccaries), Ruminantia (cows and deer), and Cetacea (whales and dolphins). (2) After divergence of the Suina lineage, the CHR-1 SINE and the CHR-2 SINE were generated suc- cessively in a common ancestor of ruminants, hippopotamuses, and cetaceans. (3) In the Ruminantia lineage, the Bov-tA SINE was generated by recombination between the CHR-2 SINE and Bov-A. (4) In the Suina lineage, the CHRS-S SINE was generated from the CHRS SINE. (5) In this latter lineage, the PRE-1 family of SINEs was created by insertion of part of the gene for tRNA Arg into the 59 region of the CHRS-S family. The distribution of a particular family of SINEs among species of artiodactyls and cetaceans confirmed the most recent conclusion for paraphyly of the order Artiodactyla. The present study also revealed that a newly created tRNA Glu -derived family of SINEs was subjected both to recombination with different units and to duplication of an internal sequence within a SINE unit to generate, during evolution, a huge superfamily of tRNA Glu -related families of SINEs that are now found in the genomes of artiodactyls and cetaceans.
A suite of comparisons among ten radiolabelled dasyurid species and one outgroup bandicoot was generated using the hydroxyapatite chromatography method of DNA-DNA hybridisation; comparisons were also made with four other dasyurid taxa. Square matrices of AT,s, AModes, and AT56;l's were compiled and corrected for reciprocity, additivity, and, in the case of AT,' s, normalised percentages of hybridisation. These matrices were analysed using the FITCH algorithm in Felsenstein's PHYLIP (Version 3.1), and all distinct topologies were jackknifed to test for internal consistency. Additionally, uncorrected AT,, AMode, and ATSOH datasets were bootstrapped and subjected to phylogenetic analysis to assess measurement imprecision. FITCH trees from folded matrices including unlabelled s'pecies or those for which heteroduplex comparisons were incomplete were also calculated and jack-knifed, both before and after correction. With the exception of limited measurements to Dasyuroides byrnei and Dasykaluta rosamondae, which showed affinities with Dasyurus spp., the final tree was fully resolved: Sminthopsis crassicaudata and S. murina, together with the more distant Planigale maculata, are the sister-group to all other dasyurids examined, which in turn comprise two clades. One of these includes Dasyurus, Dasyuroides, and Dasykaluta; the other, 'true' Antechinus (A. flavipes, A. stuartii, A. swainsonii) as a sister-group to Antechinus melanurus plus Murexia longicaudata, with Phascogale tapoatafa representing a probable sister-group to all Antechinus with Murexia. DNA-DNA hybridisation provides no support for the genus Satanellus: most of the trees linked Dasyurus albopunctatus with D. maculatus instead of D. hallucatus. Similarly, Antechinus flavipes and A. stuartii appear to be closer to each other than either is to A. swainsonii. The historical biogeographic significance of the adopted phylogeny is considered, and it is concluded that the putative early Miocene separation of Australia and New Guinea was probably too early to account for the independent evolution of the New Guinean clade.
A suite of comparisons among ten radiolabelled dasyurid species and one outgroup bandicoot was
generated using the hydroxyapatite chromatography method of DNA-DNA hybridisation; comparisons
were also made with four other dasyurid taxa. Square matrices of AT,s, AModes, and AT56;l's were
compiled and corrected for reciprocity, additivity, and, in the case of AT,'s, normalised percentages
of hybridisation. These matrices were analysed using the FITCH algorithm in Felsenstein's PHYLIP
(Version 3.1), and all distinct topologies were jackknifed to test for internal consistency. Additionally,
uncorrected AT,, AMode, and ATSOH datasets were bootstrapped and subjected to phylogenetic
analysis to assess measurement imprecision. FITCH trees from folded matrices including unlabelled
s'pecies or those for which heteroduplex comparisons were incomplete were also calculated and jackknifed,
both before and after correction. With the exception of limited measurements to Dasyuroides
byrnei and Dasykaluta rosamondae, which showed affinities with Dasyurus spp., the final tree was
fully resolved: Sminthopsis crassicaudata and S. murina, together with the more distant Planigale
maculata, are the sister-group to all other dasyurids examined, which in turn comprise two clades.
One of these includes Dasyurus, Dasyuroides, and Dasykaluta; the other, 'true' Antechinus (A. flavipes,
A. stuartii, A. swainsonii) as a sister-group to Antechinus melanurus plus Murexia longicaudata, with
Phascogale tapoatafa representing a probable sister-group to all Antechinus with Murexia. DNADNA
hybridisation provides no support for the genus Satanellus: most of the trees linked Dasyurus
albopunctatus with D. maculatus instead of D. hallucatus. Similarly, Antechinus flavipes and A. stuartii
appear to be closer to each other than either is to A. swainsonii. The historical biogeographic
significance of the adopted phylogeny is considered, and it is concluded that the putative early
Miocene separation of Australia and New Guinea was probably too early to account for the independent
evolution of the New Guinean clade.
Molecular and morphological data have important roles in
illuminating evolutionary history. DNA data often yield well resolved
phylogenies for living taxa, but are generally unattainable for
fossils. A distinct advantage of morphology is that some types of
morphological data may be collected for extinct and extant taxa.
Fossils provide a unique window on evolutionary history and may
preserve combinations of primitive and derived characters that are not
found in extant taxa. Given their unique character complexes, fossils
are critical in documenting sequences of character transformation over
geologic time and may elucidate otherwise ambiguous patterns of
evolution that are not revealed by molecular data alone. Here, we
employ a methodological approach that allows for the integration of
molecular and paleontological data in deciphering one of the most
innovative features in the evolutionary history of mammals—laryngeal
echolocation in bats. Molecular data alone, including an expanded data
set that includes new sequences for the A2AB gene, suggest that
microbats are paraphyletic but do not resolve whether laryngeal
echolocation evolved independently in different microbat lineages or
evolved in the common ancestor of bats and was subsequently lost in
megabats. When scaffolds from molecular phylogenies are incorporated
into parsimony analyses of morphological characters, including
morphological characters for the Eocene taxa
Icaronycteris, Archaeonycteris,
Hassianycteris, and Palaeochiropteryx,
the resulting trees suggest that laryngeal echolocation evolved in the
common ancestor of fossil and extant bats and was subsequently lost in
megabats. Molecular dating suggests that crown-group bats last shared a
common ancestor 52 to 54 million years ago.
The traditional views regarding the mammalian order Insectivora are that the group descended from a single common ancestor
and that it is comprised of the following families: Soricidae (shrews), Tenrecidae (tenrecs), Solenodontidae (solenodons),
Talpidae (moles), Erinaceidae (hedgehogs and gymnures), and Chrysochloridae (golden moles). Here we present a molecular analysis
that includes representatives of all six families of insectivores, as well as 37 other taxa representing marsupials, monotremes,
and all but two orders of placental mammals. These data come from complete sequences of the mitochondrial 12S rRNA, tRNA-Valine,
and 16S rRNA genes (2.6 kb). A wide range of different methods of phylogenetic analysis groups the tenrecs and golden moles
(both endemic to Africa) in an all-African superordinal clade comprised of elephants, sirenians, hyracoids, aardvark, and
elephant shrews, to the exclusion of the other four remaining families of insectivores. Statistical analyses reject the idea
of a monophyletic Insectivora as well as traditional concepts of the insectivore suborder Soricomorpha. These findings are
supported by sequence analyses of several nuclear genes presented here: vWF, A2AB, and α-β hemoglobin. These results require
that the order Insectivora be partitioned and that the two African families (golden moles and tenrecs) be placed in a new
order. The African superordinal clade now includes six orders of placental mammals.
Bats (order Chiroptera) are one of the few orders of mammals that echolocate and the only group with the capacity for powered flight. The order is subdivided into Microchiroptera and Megachiroptera, with an array of characteristics defining each group, including complex laryngeal echolocation systems in microbats and enhanced visual acuity in megabats. The respective monophylies of the two suborders have been tacitly assumed, although microbat monophyly is uncorroborated by molecular data. Here we present a phylogenetic analysis of bat relationships using DNA sequence data from four nuclear genes and three mitochondrial genes (total of 8,230 base pairs), indicating that microbat families in the superfamily Rhinolophoidea are more closely related to megabats than they are to other microbats. This implies that echolocation systems either evolved independently in rhinolophoids and other microbats or were lost in the evolution of megabats. Our data also reject flying lemur (order Dermoptera) as the bat sister group, indicating that presumed shared derived characters for flying lemurs and bats are convergent features that evolved in association with gliding and flight, respectively.
The precise hierarchy of ancient divergence events that led to the present assemblage of modern placental mammals has been an area of controversy among morphologists, palaeontologists and molecular evolutionists. Here we address the potential weaknesses of limited character and taxon sampling in a comprehensive molecular phylogenetic analysis of 64 species sampled across all extant orders of placental mammals. We examined sequence variation in 18 homologous gene segments (including nearly 10,000 base pairs) that were selected for maximal phylogenetic informativeness in resolving the hierarchy of early mammalian divergence. Phylogenetic analyses identify four primary superordinal clades: (I) Afrotheria (elephants, manatees, hyraxes, tenrecs, aardvark and elephant shrews); (II) Xenarthra (sloths, anteaters and armadillos); (III) Glires (rodents and lagomorphs), as a sister taxon to primates, flying lemurs and tree shrews; and (IV) the remaining orders of placental mammals (cetaceans, artiodactyls, perissodactyls, carnivores, pangolins, bats and core insectivores). Our results provide new insight into the pattern of the early placental mammal radiation.
A maximum likelihood method for inferring evolutionary trees from DNA sequence data was developed by Felsenstein (1981). In evaluating the extent to which the maximum likelihood tree is a significantly better representation of the true tree, it is important to estimate the variance of the difference between log likelihood of different tree topologies. Bootstrap resampling can be used for this purpose (Hasegawa et al. 1988; Hasegawa and Kishino 1989), but it imposes a great computation burden. To overcome this difficulty, we developed a new method for estimating the variance by expressing it explicitly.The method was applied to DNA sequence data from primates in order to evaluate the maximum likelihood branching order among Hominoidea. It was shown that, although the orangutan is convincingly placed as an outgroup of a human and African apes clade, the branching order among human, chimpanzee, and gorilla cannot be determined confidently from the DNA sequence data presently available when the evolutionary rate constancy is not assumed.
Molecular phylogenetic studies have resolved placental mammals into four major groups, but have not established the full hierarchy
of interordinal relationships, including the position of the root. The latter is critical for understanding the early biogeographic
history of placentals. We investigated placental phylogeny using Bayesian and maximum-likelihood methods and a 16.4-kilobase
molecular data set. Interordinal relationships are almost entirely resolved. The basal split is between Afrotheria and other
placentals, at about 103 million years, and may be accounted for by the separation of South America and Africa in the Cretaceous.
Crown-group Eutheria may have their most recent common ancestry in the Southern Hemisphere (Gondwana).
The program MRBAYES performs Bayesian inference of
phylogeny using a variant of Markov chain Monte Carlo.
Availability: MRBAYES, including the source code, documentation,
sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
Contact: johnh{at}brahms.biology.rochester.edu
where.,Abstracts,to,talks,and,posters presented,at this meeting,can be found,at www.utexas.edu/ftp/depts/systbiol/. The talks fell into three main sections, which we will now consider, followed by a summary where,we present our current best estimate of the tree for placental mammals. The Age of Intraordinal Divergences Perhaps even,more,than,the tree of re- lationships, the ages molecular divergence times are suggesting,have,caused,greatest consternation,to morphologists.,Part of this seems to be semantics. For example, when some,authors,suggest,that perissodactyls originated well back in the late Cretaceous, it is not always,clear if they mean,the stem group Perissodactyla (i.e., all species more
The mammalian order Xenarthra (armadillos, anteaters and sloths) is one of the four major clades of placentals, but it remains poorly studied from the molecular phylogenetics perspective. We present here a study encompassing most of the order's diversity in order to establish xenarthrans' intra-ordinal relationships, discuss the evolution of their morphological characters, search for their extant sister group and specify the timing of their radiation with special emphasis on the status of the controversial fossil Eurotamandua. Sequences of three genes (nuclear exon 28 of the Von Willebrand factor and mitochondrial 12S and 16S rRNAs) are compared for eight of the 13 living genera. Phylogenetic analyses confirm the order's monophyly and that of its three major lineages: armadillos (Cingulata), anteaters (Vermilingua) and sloths ('Tardigrada', renamed in 'Folivora'), and our results strongly support the grouping of hairy xenarthrans (anteaters and sloths) into Pilosa. Within placentals, Afrotheria might be the first lineage to branch off, followed by Xenarthra. The morphological adaptative convergence between New World xenarthrans and Old World pangolins is confirmed. Molecular datings place the early emergence of armadillos around the Cretaceous/Tertiary boundary, followed by the divergence between anteaters and sloths in the Early Eocene era. These Tertiary dates contradict the concept of a very ancient origin of modern xenarthran lineages. They also question the placement of the purported fossil anteater (Eurotamandua) from the Middle Eocene period of Europe with the Vermilingua and instead suggest the independent and convergent evolution of this enigmatic taxon.
Recent palaeontological discoveries and the correspondence between molecular and morphological results provide fresh insight on the deep structure of mammalian phylogeny. This new wave of research, however, has yet to resolve some important issues.
Apolipoprotein (apo)-B-100 is the ligand that mediates the clearance of low density lipoprotein (LDL) from the circulation by the apoB,E (LDL) receptor pathway. Clearance is mediated by the interaction of a domain enriched in basic amino acid residues on apoB-100 with clusters of acidic residues on the apoB,E (LDL) receptor. A model has been proposed for the LDL receptor binding domain of apoB-100 based on the primary amino acid sequence (Knott, T. J., et al. 1986. Nature. 323: 734-738). Two clusters of basic residues (A: 3147-3157 and B: 3359-3367) are apposed on the surface of the LDL particle by a disulfide bridge between Cys 3167 and 3297. Support for this single domain model has been obtained from the mapping of epitopes for anti-apoB monoclonal antibodies that block the binding of apoB to the LDL receptor. Here we test this model by comparing the nucleotide (from 9623 to 10,442) and amino acid sequence (from 3139 to 3411) of apoB-100 in seven species (human, pig, rabbit, rat, Syrian hamster, mouse, and chicken). Overall, this region is highly conserved. Cluster B maintains a strong net positive charge and is homologous across species in both primary and secondary structure. However, the net positive charge of region A is not conserved across these species, but the region remains strongly hydrophilic. The secondary structure of the region between clusters A and B is preserved, but the disulfide bond is unique to the human sequence. This study suggests that the basic region B is primarily involved in the binding of apoB-100 to the apoB,E (LDL) receptor.
Transpositions of Alu sequences, representing the most abundant primate short interspersed elements (SINE), were evaluated as molecular cladistic markers to analyze the phylogenetic affiliations among the primate infraorders. Altogether 118 human loci, containing intronic Alu elements, were PCR analyzed for the presence of Alu sequences at orthologous sites in each of two strepsirhine, New World and Old World monkey species, Tarsius bancanus, and a nonprimate outgroup. Fourteen size-polymorphic amplification patterns exhibited longer fragments for the anthropoids (New World and Old World monkeys) and T. bancanus whereas shorter fragments were detected for the strepsirhines and the outgroup. From these, subsequent sequence analyses revealed three Alu transpositions, which can be regarded as shared derived molecular characters linking tarsiers and anthropoid primates. Concerning the other loci, scenarios are represented in which different SINE transpositions occurred independently in the same intron on the lineages leading both to the common ancestor of anthropoids and to T. bancanus, albeit at different nucleotide positions. Our results demonstrate the efficiency and possible pitfalls of SINE transpositions used as molecular cladistic markers in tracing back a divergence point in primate evolution over 40 million years old. The three Alu insertions characterized underpin the monophyly of haplorhine primates (Anthropoidea and Tarsioidea) from a novel perspective.
A phylogenetic analysis of 35 mammalian taxa focusing on the lipotyphlan family Tenrecidae, based on 193 morphological character states across 71 characters, is undertaken to test several hypotheses of lipotyphlan relationships, including monophyly of the Lipotyphla, Tenrecidae, Malagasy Tenrecidae, and Caribbean Lipotyphla. Explicit tests of these hypotheses are central to understanding larger issues concerning Malagasy and Caribbean biogeography, in addition to mammalian phylogeny. Methodologically, several different parameters are created with which to determine the sensitivity of resulting clades to initial assumptions about a posteriori character weighting, missing data, and multistate character ordering. Clades produced by this data set that appear despite perturbations in these parameters and that are supported by other confidence-assessment techniques contradict Malagasy tenrecid monophyly and the association of soricids with the Caribbean taxon Solenodon. Results regarding tenrecid and lipotyphlan monophyly are more ambiguous and depend on certain assumptions regarding treatment of character ordering, weighting, and missing data. An alternative phylogeny supporting an African mammal clade receives no support from the data set discussed herein.
We concatenated sequences for four mitochondrial genes (12S rRNA, tRNA valine, 16S rRNA, cytochrome b) and four nuclear genes [aquaporin, alpha 2B adrenergic receptor (A2AB), interphotoreceptor retinoid-binding protein (IRBP),
von Willebrand factor (vWF)] into a multigene data set representing 11 eutherian orders (Artiodactyla, Hyracoidea, Insectivora,
Lagomorpha, Macroscelidea, Perissodactyla, Primates, Proboscidea, Rodentia, Sirenia, Tubulidentata). Within this data set,
we recognized nine mitochondrial partitions (both stems and loops, for each of 12S rRNA, tRNA valine, and 16S rRNA; and first,
second, and third codon positions of cytochrome b) and 12 nuclear partitions (first, second, and third codon positions, respectively, of each of the four nuclear genes). Four
of the 21 partitions (third positions of cytochrome b, A2AB, IRBP, and vWF) showed significant heterogeneity in base composition across taxa. Phylogenetic analyses (parsimony,
minimum evolution, maximum likelihood) based on sequences for all 21 partitions provide 99–100% bootstrap support for Afrotheria
and Paenungulata. With the elimination of the four partitions exhibiting heterogeneity in base composition, there is also
high bootstrap support (89–100%) for cow + horse. Statistical tests reject Altungulata, Anagalida, and Ungulata. Data set
heterogeneity between mitochondrial and nuclear genes is most evident when all partitions are included in the phylogenetic
analyses. Mitochondrial-gene trees associate cow with horse, whereas nuclear-gene trees associate cow with hedgehog and these
two with horse. However, after eliminating third positions of A2AB, IRBP, and vWF, nuclear data agree with mitochondrial data
in supporting cow + horse. Nuclear genes provide stronger support for both Afrotheria and Paenungulata. Removal of third positions
of cytochrome b results in improved performance for the mitochondrial genes in recovering these clades.
Periodically it is worthwhile to assess our knowledge and understanding of mammalian phylogeny and one of its expressions, classification. This short paper is yet another attempt to do so, taking into account the results of recently published paleontological research and drawing heavily on work in progress by many researchers in many fields and in various parts of the world. Concepts of mammalian phylogeny and classification have changed markedly during the last few years. A good many of the ideas expressed here are frankly speculative, but they are presented anyway in order to determine how well they will stand scrutiny, especially by nonpaleontologists. A few years ago I prepared a paper with a similar aim (McKenna, 1969), but that paper is now outdated. In the present offering I attempt to update certain aspects of my previous review by taking into account research published since 1969, as well as work being incorporated into a new classification of the Mammalia now being prepared which wall deal with all taxonomic levels down to the subgeneric level in essentially the same style as Simpson’s (1945) classification.
Likelihood-based statistical tests of competing evolutionary hypotheses (tree topologies) have been available for approximately
a decade. By far the most commonly used is the Kishino-Hasegawa test. However, the assumptions that have to be made to ensure
the validity of the Kishino–Hasegawa test place important restrictions on its applicability. In particular, it is only valid
when the topologies being compared are specified a priori. Unfortunately, this means that the Kishino-Hasegawa test may be
severely biased in many cases in which it is now commonly used: for example, in any case in which one of the competing topologies
has been selected for testing because it is the maximum likelihood topology for the data set at hand. We review the theory
of the Kishino-Hasegawa test and contend that for the majority of popular applications this test should not be used. Previously
published results from invalid applications of the Kishino–Hasegawa test should be treated extremely cautiously, and future
applications should use appropriate alternative tests instead. We review such alternative tests, both nonparametric and parametric,
and give two examples which illustrate the importance of our contentions.
— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
Apolipoprotein (apo) B-100, the major protein component in low density lipoprotein (LDL), is the ligand that binds to the LDL receptor1. It is important in the metabolism of LDL and elevated plasma levels of LDL-apo B are strongly associated with increased risk of coronary artery disease. Although apo B-100 is of great clinical and biological importance its primary structure has defied chemical elucidation, mainly because of its enormous size, insolubility, and tendency to aggregate2. Less than 5% of the apo B-100 sequence has been reported, despite the efforts of many laboratories over the past twenty years. Here we report the complete amino acid sequence of human apo B-100 as deducted by sequence analysis of complementary DNA clones; 2,366 of the 4,536 residues were also confirmed by direct sequencing of apo B-100 tryptic peptides. The distribution of trypsin-accessible and -inaccessible peptides of the protein on LDL is non-random and they can be grouped into 5 hypothetical domains. Of 20 potential N-glycosylation sites identified in the sequence, 13 were foundry direct peptide sequencing to be glycosylated, and 4 unglycosylated. Examination of the primary structure of apo B-100 reveals that it contains a large number of long (>70 residues) internal repeats and an even larger number of shorter ones, suggesting that the apo B-100 sequence was derived largely from internal duplications. Finally, using synthetic peptides of a specific region of apo B-100, we have identified a potential LDL receptor-binding domain (residues 3,345-3,381) which can bind to the LDL receptor and suppress 3-hydroxy-3-methyl-glutaryl coenzyme A (HMG-CoA) reductase activities in cultured human fibroblasts.
The phylogenetic relationships of the 16 species of Monarda (Lamiaceae) were investigated using sequences of the internal transcribed spacer regions of nuclear ribosomal DNA. Thymus and Mentha were used as outgroups, and Blephilia, Clinopodium, Conradina, Hesperozygis, Monardella, Pycnanthemum, and Ziziphora were included in the ingroup to test the monophyly of Monarda. Two parsimony searches were performed after removing redundant sequences from the analysis: one with indels scored as missing and a second with indels treated as binary characters. Both searches yielded congruent results, but the treatment of indels as binary characters resulted in considerably more resolution within Monarda. There was strong support for the monophyly of Monarda and a close relationship was found between Monarda, Blephilia, and Pycnanthemum. The molecular phylogeny was completely congruent with the infrageneric classification of the genus. Our results were consistent with hypotheses of hybridization between M. fistulosa and M. lindheimeri in Texas. Despite considerable morphological variation among many species, especially in floral characters, little molecular diversification was found in those same species groups. Intraspecific polymorphism in ITS sequence was found in over half the species examined, and may be attributable to ancestral polymorphism, hybridization, or detection of paralogous loci. Communicating Editor: Jim Smith
Abstract— Diverse morphological evidence from both living and fossil taxa suggests several higher-level groupings of the Recent orders of eutherian mammals. The strongest hypotheses closely relate rodents and lagomorphs within Glires, proboscideans and sirenians within Tethytheria, hyracoids and tethytheres within Paenungulata, chiropterans and dermopterans, and pholidotans and edentates. Somewhat weaker evidence supports groupings of Glires with macroscelideans, primates and tree-shrews with bats and flying lemurs (Archonta), and all Eutheria excluding pangolins and edentates (Epitheria). There is some tenuous evidence for the monophyly of all modern ungulate orders (including cetaceans), and for the division between artiodactyls and other ungulates. Rather than providing only a confusing and unresolved picture of higher eutherian relationships, comparative morphology and paleontology offer some compelling hypotheses that comprise a framework for studies of macromolecular traits.
A phylogenetic analysis of 35 mammalian taxa focusing on the lipotyphlan family Tenrecidae, based on 193 morphological character states across 71 characters, is undertaken to test several hypotheses of lipotyphlan relationships, including monophyly of the Lipotyphla, Tenrecidae, Malagasy Tenrecidae, and Caribbean Lipotyphla. Explicit tests of these hypotheses are central to understanding larger issues concerning Malagasy and Caribbean biogeography, in addition to mammalian phylogeny. Methodologically, several different parameters are created with which to determine the sensitivity of resulting clades to initial assumptions about a posteriori character weighting, missing data, and multistate character ordering. Clades produced by this data set that appear despite perturbations in these parameters and that are supported by other confidence-assessment techniques contradict Malagasy tenrecid monophyly and the association of soricids with the Caribbean taxon Solenodon. Results regarding tenrecid and lipotyphlan monophyly are more ambiguous and depend on certain assumptions regarding treatment of character ordering, weighting, and missing data. An alternative phylogeny supporting an African mammal clade receives no support from the data set discussed herein.
Following consideration of 20 morphological parameters of the gastrointestinal tract of ungulates and Cetacea, as well as of the production of methane, phylogenetic trees were constructed for baleen whales (Mysticeti), toothed whales (Odontoceti) and beaked whales (Ziphiidae), as well as for four taxa of the PSHM group (Fischer and Tassy: in Szalay, F. S.; Novacek, M. J.; McKenna, M. C. (eds), Mammal Phylogeny, Placentals. New York, Berlin: Springer Verlag, pp. 217–234, 1993), the Proboscidea (elephants), Sirenia (sea cows), Hyracoidea (hyraxes) and the Equidae (horses and their kin) as representatives of the Mesaxonia. In addition five families of the Artiodactyla, namely, pigs (Suidae), peccaries (Tayassuidae), hippos (Hippopotamidae), camels and their South American kin (Camelidae), chevrotains (Tragulidae) as well as ruminants with horns or antlers (Pecora) were considered. Insectivores without a caecum (Lipotyphla) were included as an outgroup. The following interrelationship for the considered taxa was found ( Fig. 8a):
Part of the 12S rDNA gene was amplified and sequenced for 11 placental mammals, 3 marsupials, and 2 monotremes. Multiple alignments for these sequences and nine additional placental sequences taken from GenBank were obtained using CLUSTAL. Phylogenetic analyses were performed using standard parsimony, transversion parsimony, and Lake's method of invariants. All of our analyses uniteLoxodontia withDugong. Procavia, in turn, is a sister group to these taxa, thus supporting the monophyly of the Paenungulata. Perissodactyls are a sister group to paenungulates when transitions and transversions are both included but not when transitions are omitted. Likewise, cetaceans are a sister group to artiodactyls on minimum length trees under standard parsimony but not under transversion parsimony. Rodent monophyly and bat monophyly also receive mixed support, as does a putative alliance between primates and lagomorphs. Interestingly, the percentage divergence between the echidna and the platypus is less than for the rat and mouse.
Hyracoids have been allied with either perissodactyls or tethytheres (i.e., Proboscidea + Sirenia) based on morphological data. The latter hypothesis, termed Paenungulata, is corroborated by numerous molecular studies. However, molecular studies have failed to support Tethytheria, a group that is supported by morphological data. We examined relationships among living paenungulate orders using a multigene data set that included sequences from four mitochondrial genes (12S rRNA, tRNA valine, 16S rRNA, cytochrome b) and four nuclear genes (aquaporin, A2AB, IRBP, vWF). Nineteen maximum-likelihood models were employed, including models with process partitions for base composition and substitution parameterizations. With the inclusion of partitions with a heterogeneous base composition, 18 of 19 models favored Hyracoidea + Sirenia. All 19 models favored Hyracoidea + Sirenia after excluding heterogeneous base composition partitions. Most of the support for Hyracoidea + Sirenia derived from the mitochondrial genes (bootstrap support ranged from 51 to 99%); Tethytheria, in turn, received 0 to 19% support in different analyses. Bootstrap support deriving from the nuclear genes was more evenly split among the competing hypotheses (3 to 45% for Tethytheria; 17.5 to 62% for Hyracoidea + Sirenia). Lineage-specific rate variation among both mitochondrial and nuclear genes may contribute to the different results that were obtained with mitochondrial versus nuclear data. Whether Tethytheria or a competing hypothesis is correct, short internodes on the molecular phylogenies suggest that paenungulate orders diverged from each other over a 5- to 8-million-year time window extending from the late Paleocene into the early Eocene. We also used likelihood-ratio tests to compare different models of sequence evolution. A gamma distribution of rates results in a greater improvement in likelihood scores than does an allowance for invariant sites. Twenty-one rate partitions corresponding to stems, loops, and codon positions of different genes result in higher likelihood scores than a gamma distribution of rates and/or an allowance for invariant sites. Process partitions of the data that incorporate base composition and substitution parameterizations result in significant improvements in likelihood scores in comparison to models that allow only for relative rate differences among partitions.
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.
The sequence of the mitochondrial DNA (mtDNA) molecule of the European hedgehog (Erinaceus europaeus) was determined. The length of the sequence presented is 17,442 nucleotides (nt). The molecule is thus the largest eutherian mtDNA molecule so far reported. The organization of the molecule conforms with that of other eutherians, but the control region of the molecule is exceptionally long, 1,988 nt, due to the presence of repeated motifs at two different positions in the 3 part of the control region. The length of the control region is not absolute due to pronounced heteroplasmy caused by variable numbers of the motif TACGCA in one of the repetitive regions. The sequence presented includes 46 repeats of this type. The other repeated region is composed of different AT-rich repeats. This region was identical among four clones studied. Comparison of mitochondrial peptide-coding genes identified a separate position of the hedgehog among several mammalian orders. The concatenated protein sequence of the 13 peptide-coding genes was used in a phylogenetic study using the opossum as outgroup. The position of the hedgehog sequence was basal among the other eutherian sequences included: human, rat, mouse, cow, blue whale, harbor seal, and horse. The analysis did not resolve the relationship among carnivores, perissodactyls, and artiodactyls/cetaceans, suggesting a closer relationship among these orders than acknowledged by classical approaches.
Higher-level relationships among placental mammals, as well as the historical biogeography of this group against the backdrop of continental fragmentation and reassembly, remain poorly understood. Here, we analyze two independent molecular data sets that represent all placental orders. The first data set includes six genes (A2AB, IRBP, vWF, 12S rRNA, tRNA valine, 16S rRNA; total = 5.71 kb) for 26 placental taxa and two marsupials; the second data set includes 2.95 kb of exon 11 of the BRCA1 gene for 51 placental taxa and four marsupials. We also analyzed a concatenation of these data sets (8.66 kb) for 26 placentals and one marsupial. Unrooted and rooted analyses were performed with parsimony, distance methods, maximum likelihood, and a Bayesian approach. Unrooted analyses provide convincing support for a fundamental separation of placental orders into groups with southern and northern hemispheric origins according to the current fossil record. On rooted trees, one or both of these groups are monophyletic depending on the position of the root. Maximum likelihood and Bayesian analyses with the BRCA1 and combined 8.66 kb data sets provide strong support for the monophyly of the northern hemisphere group (Boreoeutheria). Boreoeutheria is divided into Laurasiatheria (Carnivora + Cetartiodactyla + Chiroptera + Eulipotyphla + Perissodactyla + Pholidota) and Euarchonta (Dermoptera + Primates + Scandentia) + Glires (Lagomorpha + Rodentia). The southern hemisphere group is either monophyletic or paraphyletic, depending on the method of analysis used. Within this group, Afrotheria (Proboscidea + Sirenia + Hyracoidea + Tubulidentata + Macroscelidea + Afrosoricida) is monophyletic. A unique nine base-pair deletion in exon 11 of the BRCA1 gene also supports Afrotheria monophyly. Given molecular dates that suggest that the southern hemisphere group and Boreoeutheria diverged in the Early Cretaceous, a single trans-hemispheric dispersal event may have been of fundamental importance in the early history of crown-group Eutheria. Parallel adaptive radiations have subsequently occurred in the four major groups: Laurasiatheria, Euarchonta + Glires, Afrotheria, and Xenarthra.
A solution to higher level mammalian phylogeny is going to depend on the congruent establishment of superordinal groupings followed by a linking together of these clades. We present congruent and convincing evidence from four disparate nuclear protein coding genes and from a tandem alignment of the 12S–16S mitochondrial region, for a superordinal clade of endemic African mammals that includes elephant shrews, aardvarks, golden mole, elephants, sirenians, and hyraxes. Because of strong support for golden mole as part of this clade, the Insectivora are rendered paraphyletic or polyphyletic, with constrained monophyly of the insectivores judged significantly worse in the vast majority of tests. Branching arrangement within this clade remains highly uncertain; however, a tandem alignment of the protein coding genes suggests elephant shrew is the earliest African lineage. None of the individual data sets or combinations of data sets support the widely held view of a mirorder Tethytheria (Sirenia/Proboscidea), although only a tandem alignment of protein coding and mitochondrial loci significantly rejects this association. The majority of the data sets and analyses provide strong support for Caviomorpha as part of a monophyletic Rodentia.
A highly resolved primate cladogram based on DNA evidence is congruent with extant and fossil osteological evidence. A provisional primate classification based on this cladogram and the time scale provided by fossils and the model of local molecular clocks has all named taxa represent clades and assigns the same taxonomic rank to those clades of roughly equivalent age. Order Primates divides into Strepsirhini and Haplorhini. Strepsirhines divide into Lemuriformes and Loriformes, whereas haplorhines divide into Tarsiiformes and Anthropoidea. Within Anthropoidea when equivalent ranks are used for divisions within Platyrrhini and Catarrhini, Homininae divides into Hylobatini (common and siamang gibbon) and Hominini, and the latter divides into Pongina forPongo(orangutans) and Hominina forGorillaandHomo. Homoitself divides into the subgeneraH.(Homo) for humans andH.(Pan) for chimpanzees and bonobos. The differences between this provisional age related phylogenetic classification and current primate taxonomies are discussed.
The origin of whales and their transition from terrestrial life to a fully aquatic existence has been studied in depth. Palaeontological, morphological and molecular studies suggest that the order Cetacea (whales, dolphins and porpoises) is more closely related to the order Artiodactyla (even-toed ungulates, including cows, camels and pigs) than to other ungulate orders. The traditional view that the order Artiodactyla is monophyletic has been challenged by molecular analyses of variations in mitochondrial and nuclear DNA. We have characterized two families of short interspersed elements (SINEs) that were present exclusively in the genomes of whales, ruminants and hippopotamuses, but not in those of camels and pigs. We made an extensive survey of retropositional events that might have occurred during the divergence of whales and even-toed ungulates. We have characterized nine retropositional events of a SINE unit, each of which provides phylogenetic resolution of the relationships among whales, ruminants, hippopotamuses and pigs. Our data provide evidence that whales, ruminants and hippopotamuses form a monophyletic group.
The evolutionary relationships of the various orders of placental mammals remain an issue of uncertainty and controversy. Molecular studies of mammalian phylogeny at the DNA level that include more than just a few orders are still relatively meager. Here we report results on mammalian phylogeny deduced from the coding sequence of the single-copy nuclear gene for the interphotoreceptor retinoid binding protein (IRBP). Analysis of 13 species representing eight eutherian orders and one marsupial yielded results that falsify the hypothesis that megachiropteran bats are "flying primates," only convergently resembling microchiropteran bats. Instead, in agreement with more traditional views, as well as those from other recent molecular studies, the results strongly support a monophyletic Chiroptera (micro- and megabats grouped together). The IRBP results also offer some rare molecular support for the Glires concept, in which rodents and lagomorphs form a superordinal grouping. Also in congruence with other recent molecular evidence, IRBP sequences do not support the view of a superorder Archonta that includes Chiroptera along with Dermoptera (flying lemur), Scandentia (tree shrew), and Primates. IRBP was not however, without its shortcomings as a molecular phylogenetic system: high levels of homoplasy, evident in the marsupial outgroup, did not allow us to properly root the tree, and several of the higher level eutherian clades were only weakly supported (e.g., a Carnivora/Chiroptera clade and an Artiodactyla/Carnivora/Chiroptera clade). We suggest that these shortcomings may be diminished as the phylogenetic density of the data set is increased.
For the past 5 years, investigators from many different laboratories have contributed to a greatly increased understanding of two very important lipid-carrying proteins in plasma--apo B-100 and apo B-48. Apo B-100, an extremely large protein composed of 4,536 amino acids, is synthesized by the liver and is crucial for the assembly of triglyceride-rich VLDL particles. Apo B-100 is virtually the only protein of LDL, a cholesteryl ester-enriched class of lipoproteins that are metabolic products of VLDL. The apo B-100 of LDL serves as a ligand for the LDL receptor-mediated uptake of LDL particles by the liver and extrahepatic tissues. The LDL receptor-binding region of apo B-100 is located in the carboxyterminal portion of the molecule, whereas its lipid-binding regions appear to be broadly dispersed throughout its length. Apo B-48 contains the amino-terminal 2,152 amino acids of apo B-100 and is produced by the intestine as a result of editing of a single nucleotide of the apo B mRNA, which changes the codon specifying apo B-100 amino acid 2,153 to a premature stop codon. Apo B-48 has an obligatory structural role in the formation of chylomicrons; therefore, its synthesis is essential for absorption of dietary fats and fat-soluble vitamins. Both apo B-48 and apo B-100 are encoded on chromosome 2 by a single gene that contains 29 exons and 28 introns. An elevated level of apo B-100 in the plasma is a potent risk factor for developing premature atherosclerotic disease. In the past 3 years, many different apo B gene mutations that affect the concentrations of both apo B and cholesterol in the plasma have been characterized. A missense mutation in the codon for apo B-100 amino aid 3,500 is associated with hypercholesterolemia. This mutation results in poor binding of apo B-100 to the LDL receptor, thereby causing the cholesteryl ester-enriched LDL particles to accumulate in the plasma. This disorder is called familial defective apo B-100, and it is probably a cause of premature atherosclerotic disease. Familial hypobetalipoproteinemia is a condition associated with abnormally low levels of apo B and cholesterol; affected individuals may actually have a reduced risk of atherosclerotic disease.(ABSTRACT TRUNCATED AT 400 WORDS)
Immunologically defined alleles of the pig apolipoprotein B (ApoB) locus (apoB) are correlated with different blood cholesterol levels and predisposition towards premature coronary heart disease. We show here that these alleles are associated with differences in the apoB gene by identifying six restriction fragment length polymorphisms at the pig apoB locus. We have sequenced a 2.4-kb fragment encompassing exons 11 through 14 of one allele, and 7.1 kb from the 3' one-third of exon 26 to about 1 kb past the last exon from another allele. The decoded amino acids of the pig and human ApoB proteins are identical at 70% of these positions. One region close to the C-terminus of the protein is surprisingly different in pigs and humans (57% identity) but the C-terminal region is relatively well conserved (74% identity). Neither of the two putative low-density lipoprotein (LDL) receptor-binding sites is completely conserved in pigs and humans, but identical stretches of amino acids occur near these sites more frequently than in the other sequenced regions. We compare the nucleotide sequences of the region encompassing the putative LDL receptor-binding sites from four pig alleles, including one implicated directly in atherosclerosis. None of the differences appears to account for the hypercholesterolemic phenotype. We conclude that significant differences in the physiology of LDL particles result from changes outside the putative receptor-binding region.