Phylogenetic assessment of molecular and morphological data for eutherian mammals

The interordinal relationships of eutherian (placental) mammals were evaluated by a phylogenetic analysis of four published data sets (three sequences and one morphological). The nature and degree of support and conflict for particular groups were assessed by separate bootstrap and homogeneity tests, which were followed by combined analyses of the sequence and morphological data. Between orders, strong support (i.e., > or = 95% bootstrap scores) was found for a paraphyletic Artiodactyla (relative to Cetacea) and a monophyletic Cetartiodactyla (Artiodactyla and Cetacea) and Paenungulata (Hyracoidea, Proboscidea, and Sirenia). In turn, some reasonable to strong evidence (> or = 85%) was obtained for Hyracoidea with Sirenia, Dermoptera with Scandentia, Glires (Lagomorpha with Rodentia), and Afrotheria (Amblysomus, Macroscelidea, Paenungulata, and Tubulidentata). Otherwise, no other interordinal clades were supported at these reasonable to strong levels. This overall lack of resolution for eutherian interordinal clusters agrees with other studies that suggest further progress will continue to be slow and difficult. Further resolution will require the integration of more recently published data, the continued sampling of taxa and characters, and the use of more powerful methods of data analysis.     

Chromosome painting among Proboscidea, Hyracoidea and Sirenia: support for Paenungulata (Afrotheria, Mammalia) but not Tethytheria

Despite marked improvements in the interpretation of systematic relationships within Eutheria, particular nodes, including Paenungulata (Hyracoidea, Sirenia and Proboscidea), remain ambiguous. The combination of a rapid radiation, a deep divergence and an extensive morphological diversification has resulted in a limited phylogenetic signal confounding resolution within this clade both at the morphological and nucleotide levels. Cross-species chromosome painting was used to delineate regions of homology between Loxodonta africana (2n=56), Procavia capensis (2n=54), Trichechus manatus latirostris (2n=48) and an outgroup taxon, the aardvark (Orycteropus afer, 2n=20). Changes specific to each lineage were identified and although the presence of a minimum of 11 synapomorphies confirmed the monophyly of Paenungulata, no change characterizing intrapaenungulate relationships was evident. The reconstruction of an ancestral paenungulate karyotype and the estimation of rates of chromosomal evolution indicate a reduced rate of genomic repatterning following the paenungulate radiation. In comparison to data available for other mammalian taxa, the paenungulate rate of chromosomal evolution is slow to moderate. As a consequence, the absence of a chromosomal character uniting two paenungulates (at the level of resolution characterized in this study) may be due to a reduced rate of chromosomal change relative to the length of time separating successive divergence events.     

Additional support for Afrotheria and Paenungulata,the performance of mitochondrial versus nuclear genes,and the impact of data partitions with heterogeneous base composition

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.     

Maximum-Likelihood Analysis of the Tethythere Hypothesis Based on a Multigene Data Set and a Comparison of Different Models of Sequence Evolution

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.     

Chromosome painting in the manatee supports Afrotheria and Paenungulata

Background  

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

A retroposon analysis of Afrotherian phylogeny

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

The primary structure of the hemoglobin of the Brazilian manatee (Trichechus inunguis, Sirenia)

The hemoglobin of the Brazilian Manatee (Trichechus inunguis, Sirenia) consists of one component. We present the primary structures of the alpha- and beta-chains which have been separated by chromatography on carboxymethyl-cellulose CM-52. The sequences have been determined by automatic Edman degradation with the film technique, using the native chains, tryptic peptides and the C-terminal prolyl-peptide obtained by acid hydrolysis of the Asp-Pro bond of the alpha-chains. Compared to the corresponding human chains we found 27 substitutions in the alpha- as well as in the beta-chains. Three heme contacts and four alpha 1/beta 1 contacts between the subunits are affected by exchanges. The hemoglobin of Trichechus inunguis is compared with those of Elephas maximus, Loxodonta africana, and Procavia habessinica and the monophyletic origin of the superorder Paenungulata is discussed.     

PHYLOGENY OF PRIMATES AND OTHER EUTHERIAN ORDERS: A CLADISTIC ANALYSIS USING AMINO ACID AND NUCLEOTIDE SEQUENCE DATA

Abstract— Genealogical reconstructions carried out by the parsimony method on protein amino acid and DNA nucleotide sequence data are providing fresh evidence on cladistic branching patterns at taxonomic levels from the classes of Vertebrata and orders of Eutheria to the genera of Hominoidea. Minimum length trees constructed from amino acid sequence data group Mammalia with Archosauria (i.e., Aves plus Crocodilia), Amniota with Amphibia, and Tetrapoda with Teleostei. Within Mammalia, Edentata and Paenungulata (e.g., Proboscidea) appear as the most anciently separated from other eutherians. Another superordinal eutherian clade consists of Artiodactyla, Cetacea, and Perissodactyla. A third consistently contains Primates, Lagomorpha, and Tupaia. The cladistic positions of such orders as Carnivora, Chiroptera, Insectivora, and Rodentia are not well resolved by the currently still sparse body of sequence data. However, recent dramatic progress in the technology of gene cloning and nucleotide sequencing has opened the way for so enlarging the body of sequence data that it should become possible to solve almost any problem concerning the phylogenetic systematice of extant mammals. An example is provided by hominoid genera. Minimum length trees constructed from mitochondrial DNA nucleotide sequence data very strongly group Pan, Homo , and Gorilla into Homininae and then join Homininae and Ponginae (pongo) into Hominidae as the sister family of Hylobatidae (Hylobates). Resolution of the hominine trichotomy into two dichotomous branchings should be forthcoming as kilobase sequencing of nuclear genes progresses.     

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

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

Molecular Evidence for the Major Clades of Placental Mammals

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.     

Mitogenomic analyses of eutherian relationships

Reasonably correct phylogenies are fundamental to the testing of evolutionary hypotheses. Here, we present phylogenetic findings based on analyses of 67 complete mammalian mitochondrial (mt) genomes. The analyses, irrespective of whether they were performed at the amino acid (aa) level or on nucleotides (nt) of first and second codon positions, placed Erinaceomorpha (hedgehogs and their kin) as the sister group of remaining eutherians. Thus, the analyses separated Erinaceomorpha from other traditional lipotyphlans (e.g., tenrecs, moles, and shrews), making traditional Lipotyphla polyphyletic. Both the aa and nt data sets identified the two order-rich eutherian clades, the Cetferungulata (comprising Pholidota, Carnivora, Perissodactyla, Artiodactyla, and Cetacea) and the African clade (Tenrecomorpha, Macroscelidea, Tubulidentata, Hyracoidea, Proboscidea, and Sirenia). The study corroborated recent findings that have identified a sister-group relationship between Anthropoidea and Dermoptera (flying lemurs), thereby making our own order, Primates, a paraphyletic assembly. Molecular estimates using paleontologically well-established calibration points, placed the origin of most eutherian orders in Cretaceous times, 70-100 million years before present (MYBP). The same estimates place all primate divergences much earlier than traditionally believed. For example, the divergence between Homo and Pan is estimated to have taken place approximately 10 MYBP, a dating consistent with recent findings in primate paleontology.     

The chromosomes of afrotheria and their bearing on Mammalian genome evolution

Afrotheria is the clade of placental mammals that, together with Xenarthra, Euarchontoglires and Laurasiatheria, represents 1 of the 4 main recognized supraordinal eutherian clades. It reunites 6 orders of African origin: Proboscidea, Sirenia, Hyracoidea, Macroscelidea, Afrosoricida and Tubulidentata. The apparently unlikely relationship among such disparate morphological taxa and their possible basal position at the base of the eutherian phylogenetic tree led to a great deal of attention and research on the group. The use of biomolecular data was pivotal in Afrotheria studies, as they were the basis for the recognition of this clade. Although morphological evidence is still scarce, a plethora of molecular data firmly attests to the phylogenetic relationship among these mammals of African origin. Modern cytogenetic techniques also gave a significant contribution to the study of Afrotheria, revealing chromosome signatures for the group as a whole, as well as for some of its internal relationships. The associations of human chromosomes HSA1/19 and 5/21 were found to be chromosome signatures for the group and provided further support for Afrotheria. Additional chromosome synapomorphies were also identified linking elephants and manatees in Tethytheria (the associations HSA2/3, 3/13, 8/22, 18/19 and the lack of HSA4/8) and elephant shrews with the aardvark (HSA2/8, 3/20 and 10/17). Herein, we review the current knowledge on Afrotheria chromosomes and genome evolution. The already available data on the group suggests that further work on this apparently bizarre assemblage of mammals will provide important data to a better understanding on mammalian genome evolution.     

Mitogenomic relationships of placental mammals and molecular estimates of their divergences

Molecular analyses of the relationships of placental mammals have shown a progressive congruence between mitogenomic and nuclear phylogenies. Some inconsistencies have nevertheless persisted, notably with respect to basal divergences. The current study has aimed to extend the representation of groups, whose position in the placental tree has been difficult to establish in mitogenomic studies. Both ML (maximum likelihood) and Bayesian analyses identified four basal monophyletic groups, Afroplacentalia (=Afrotheria: Hyracoidea, Proboscidea, Sirenia, Tenrecidea, Tubulidentata, Macroscelidea, Chrysochloridea), Xenarthra, Archontoglires (Primates, Dermoptera, Scandentia, Lagomorpha, Rodentia) and Laurasiaplacentalia (Lipotyphla, Chiroptera, Pholidota, Carnivora, Perissodactyla, Artiodactyla, Cetacea). All analyses joined Archontoglires and Laurasiaplacentalia on a common branch (Boreoplacentalia), but the relationship between Afroplacentalia, Xenarthra and Boreoplacentalia was not conclusively resolved. The phylogenomic hypothesis with a sister group relationship between Notoplacentalia (Afroplacentalia/Xenarthra) and Boreoplacentalia served as the basis for estimating the times of placental divergences using paleontologically well-supported mammalian calibration points. These estimates placed the basal placental divergence between Boreoplacentalia and Notoplacentalia at approximately 102 MYA (million years ago). The current estimates of ordinal placental divergences are congruent with recent estimates based on nuclear data, but inconsistent with paleontological notions that have placed the origin of essentially all placental orders within an interval of 5-10 MY in the early Tertiary. Among less deep divergences the estimates placed the split between Gorilla and Pan/Homo at approximately 11.5 MYA and that between Pan and Homo at approximately 8 MYA. As a consequence of these estimates, which are in accord with recent progress in primate paleontology, the earliest divergences among recent humans become placed approximately 270,000 years ago, i.e. approximately 100,000 years earlier than the traditional age of "Mitochondrial Eve". Comparison between the two new mt genomes of Hylomys suillus (short-tailed gymnure) patently demonstrates the inconsistency that may exist between taxonomic designations and molecular difference, as the distance between these two supposedly conspecific genomes exceeds that of the three elephantid genera Elephas, Mammuthus and Loxodonta. In accordance with the progressive use of the term Placentalia for extant orders and extinct taxa falling within this group we forward new proposals for the names of some superordinal clades of placental mammals.     

Higher Taxonomic Relationships among Extant Mammals Based on Morphology, with Selected Comparisons of Results from Molecular Data

Until a few decades ago, phylogenetic relationships among placental orders were ambiguous and usually depicted to radiate as an unresolved “bush.” Resolution of this bush by various workers has been progressing slowly, but with promising results corroborated by nondental, dental, and molecular characters. In this study we continue to seek resolution. A total of 258 nondental and 2 dental characters was analyzed by PAUP and MacClade on 39 vertebrate taxa (3 reptiles, 1 nonmammalian therapsid, and 35 mammals; 20 of the mammals are extant and 15 are extinct) to study higher taxonomic relationships with emphasis on Placentalia (Eutheria). About two-thirds of the characters are osteological, the rest concern soft tissues, including myological but excluding molecular characters (most are our data, the rest are from the literature). Cladistic analysis included all 39 taxa (fossil taxa help to evaluate polarities of characters) and all characters were given equal weight. Extant Mammalia are divided into Prototheria and Theria, the latter into Marsupialia and Placentalia. Placentalia comprises Xenarthra and Epitheria. Within Epitheria, Lipotyphla and Preptotheria (emended) are sister-taxa. Preptotherian taxa group into: ungulate-related taxa and various nonungulates. The former include Carnivora, Pholidota, Tubulidentata, Artiodactyla, Cetacea, Perissodactyla, Hyracoidea, Proboscidea, and Sirenia. A possible association to embrace Lagomorpha, Rodentia, Macroscelidea, Scandentia, Primates, Chiroptera, and Dermoptera is suggested. Significant differences between our findings and those of recent investigators include the dissociation of Pholidota from Xenarthra and the plesiomorphous position of Lipotyphla within Epitheria. Congruence between morphological and molecular results is closer than previously reported.     

The primary structure of hemoglobins of the rock hyrax (Procavia habessinica, Hyracoidea): insertion of glutamine in the alpha chains

The chromatography of the hemoglobin of the rock hyrax (Procavia habessinica) gives two components (73% HbI and 27% HbII). The amino-acid analysis and the sequences of the globin chains elucidated with the phenylthiohydantoin method, did not show any differences between the alpha I and alpha II or beta I and beta II chains, respectively. The different chromatographical behaviour cannot be explained. After chain separation by chromatography on CM-52 cellulose, all four primary structures were elucidated automatically in a sequenator on the chains and the tryptic peptides. In 20% of the beta I chains the N-terminal valine was blocked by acetyl. The alignment was performed by homology with the chains of human adult hemoglobin. The alpha chain of the rock hyrax has 142 amino-acid residues, i.e. one residue more than normal mammalian alpha chains, caused by an insertion of glutamine in the GH region supposed between positions 115 and 116. A comparison of human and hyrax hemoglobins shows an exchange of 21 amino-acid residues in the alpha chains and of 24 in the beta chains. Some substitutions in alpha 1 beta 1 contacts and in the surrounding of the heme are not supposed to effect the function of the hemoglobin. The phylogenetic relationship between the rock hyrax and the Indian elephant (Elephas maximus) on the one hand and with some Perissodactyla on the other, is discussed. Up to now the exchanges of alpha 110(G17)Ala leads to Ser and beta 56(D7)Gly leads to His have only been found in hyrax and elephant. This indicates a certain relationship between Hyracoidea and Proboscidea.     

Reason for externalization of the testis of mammals

Testes externalized in a scrotum are found only in those mammals whose present lifestyle (or that of their ancestors) involves jumping, leaping or galloping, thereby creating concussive hydrostatic rises in peritoneal pressure. This would be expected to expel the contents of the reproductive tract since it does not possess a sphincter. The lower temperature of the externalized testes is then seen as a secondary adjuvant adaptation to a cooler location than within the body cavity. The theory also explains the close phylogenetic relationship between the Proboscidea, Hyracoidea, and Sirenia, if it is assumed that their common ancestor was not endowed with the genes necessary for externalization.     

Highly Congruent Molecular Support for a Diverse Superordinal Clade of Endemic African Mammals

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.     

Phylogenetic relationships of the New World Troidini swallowtails (Lepidoptera: Papilionidae) based on COI, COII, and EF-1alpha genes

A phylogeny of the Neotropical members of the Tribe Troidini (Lepidoptera: Papilionidae) was obtained with sequences of three protein-coding genes: two mitochondrial (COI and COII), and one nuclear (EF-1alpha). Parsimony and Bayesian analyses of 33 taxa resulted in very similar trees regardless of method used with the 27 troidines always forming a monophyletic clade. Within Troidini, the genus Battus is sister group to the remaining troidines, followed by a clade formed by the Paleotropical taxa (here represented by three exemplars). The genus Euryades is the next branch, and sister group of Parides. The genus Parides is monophyletic, and is divided into four main groups by Maximum Parsimony analysis, with the most basal group composed of tailed species restricted to SE Brazil. Character optimization of ecological and morphological traits over the phylogeny proposed for troidines indicated that the use of several species of Aristolochia is ancestral over the use of few or a single host-plant. For the other three characters, the ancestral states were the absence of long tails, forest as the primary habitat and oviposition solitary or in loose group of several eggs.     

Molecular systematics of a speciose, cosmopolitan songbird genus: defining the limits of, and relationships among, the Turdus thrushes

The avian genus Turdus is one of the most speciose and widespread of passerine genera. We investigated phylogenetic relationships within this genus using mitochondrial DNA sequence data from the ND3, ND2 and cytochrome b genes. Our sampling of Turdus included 60 of the 65 extant species currently recognized, as well as all four species from three genera previously shown to fall inside Turdus (Platycichla, Nesocichla, and Cichlherminia). Phylogenetic trees based on maximum likelihood and maximum parsimony algorithms were congruent. Most of the Turdus taxa sampled fall into one of four clades: an African clade, a Central American-Caribbean clade, a largely South American clade, and a Eurasian clade. Still other taxa are placed either at the base of Turdus, or as links between clades. In no instance is any continent reciprocally monophyletic for the species distributed on it. A general lack of nodal support near the base of the phylogeny seems related to a rapid intercontinental establishment of the major clades within Turdus very early in the history of the genus. The monotypic genus Psophocichla is distantly related to, but clearly the sister of, Turdus rather than a constituent member of it.     

The position of Cetacea within mammalia: phylogenetic analysis of morphological data from extinct and extant taxa

Knowledge of the phylogenetic position of the order Cetacea (whales, dolphins, and porpoises) within Mammalia is of central importance to evolutionary biologists studying the transformations of biological form and function that accompanied the shift from fully terrestrial to fully aquatic life in this clade. Phylogenies based on molecular data and those based on morphological data both place cetaceans among ungulates but are incongruent in other respects. Morphologists argue that cetaceans are most closely related to mesonychians, an extinct group of terrestrial ungulates. They have disagreed, however, as to whether Perissodactyla (odd-toed ungulates) or Artiodactyla (even-toed ungulates) is the extant clade most closely related to Cetacea, and have long maintained that each of these orders is monophyletic. The great majority of molecule-based phylogenies show, by contrast, not only that artiodactyls are the closest extant relatives of Cetacea, but also that Artiodactyla is paraphyletic unless cetaceans are nested within it, often as the sister group of hippopotamids. We tested morphological evidence for several hypotheses concerning the sister taxon relationships of Cetacea in a maximum parsimony analysis of 123 morphological characters from 10 extant and 30 extinct taxa. We advocate treating certain multistate characters as ordered because such a procedure incorporates information about hierarchical morphological transformation. In all most-parsimonious trees, whether multistate characters are ordered or unordered, Artiodactyla is the extant sister taxon of Cetacea. With certain multistate characters ordered, the extinct clade Mesonychia (Mesonychidae + Hapalodectidae) is the sister taxon of Cetacea, and Artiodactyla is monophyletic. When all fossils are removed from the analysis, Artiodactyla is paraphyletic with Cetacea nested inside, indicating that inclusion of mesonychians and other extinct stem taxa in a phylogenetic analysis of the ungulate clade is integral to the recovery of artiodactyl monophyly. Phylogenies derived from molecular data alone may risk recovering inconsistent branches because of an inability to sample extinct clades, which by a conservative estimate, amount to 89% of the ingroup. Addition of data from recently described astragali attributed to cetaceans does not overturn artiodactyl monophyly.