Evolutionary affinities of the order Perissodactyla and the phylogenetic status of the superordinal taxa Ungulata and Altungulata

Phylogenomics reveals an almost perfect polytomy among the almost ungulates (Paenungulata)

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.

First report and genomic characterization of a bovine-like coronavirus causing enteric infection in an odd-toed non-ruminant species (Indonesian tapir, Acrocodia indica) during an outbreak of winter dysentery in a zoo

Bovine coronavirus (BCoV) is associated with three distinct clinical syndromes in cattle that is, neonatal diarrhoea, haemorrhagic diarrhoea in adults (the so-called winter dysentery syndrome, WD) and respiratory infections in cattle of different ages. In addition, bovine-like CoVs have been detected in various species including domestic and wild ruminants. However, bovine-like CoVs have not been reported so far in odd-toed ungulates. We describe an outbreak of WD associated with a bovine-like CoV affecting several captive wild ungulates, including Indonesian tapirs (Acrocodia indica) an odd-toed ungulate species (Perissodactyla) which, with even-toed ungulates species (Artiodactyla) form the clade Euungulata. Genomic characterization of the CoV revealed that it was closely related to BCoVs previously reported in America. This case illustrates the adaptability of bovine-like CoVs to new species and the necessity of continued surveillance of bovine-like CoVs in various species.

Comparative analysis of steroids in cyclic and pregnant killer whales, beluga whales and bottlenose dolphins by liquid chromatography tandem mass spectrometry

There exists a surprising diversity in the physiology and endocrinology of pregnancy among mammals in both the source (luteal/placental) and metabolism of progesterone. To evaluate the possible diversity of steroid metabolism within toothed cetaceans, we investigated 5α-reduced progesterone metabolites and androgens in cyclic (luteal phase) and pregnant captive killer whales, belugas and bottlenose dolphins (n = 5/species) bled longitudinally in early, mid- and late pregnancy (0.16, 0.50 and 0.85 fractions of 535, 464 and 380 gestation days, respectively). Mid-luteal samples were also collected. Serum was analyzed by liquid chromatography tandem-mass spectrometry as previously validated for (among others) progesterone, 20αOH-progesterone (20αOHP), 5α-dihydroprogesterone (DHP), several additional 5α-reduced metabolites and androgens (dehydroepiandrosterone, androstenedione and testosterone). The predominant mid-luteal pregnanes were: progesterone, belugas; progesterone and 20αOHP, dolphins; allopregnanolone (3α-DHP) and progesterone, killer whales. Progesterone was 2-4-fold higher in early pregnancy than mid-luteal samples but decreased thereafter. The predominant metabolite, 3β,20α-dihydroprogesterone (3β,20α-DHP; 40-80 ng/ml) was higher in mid- and late-than early gestation in all 3 species. Concentrations of 20αOHP and 3β,20α-DHP were similar at mid-gestation but 20αOHP declined in late-gestation in killer whales, and 20αOHP was lower than 3β,20α-DHP in belugas and dolphins throughout gestation. Other 5α-reduced metabolites, DHP, 3α-DHP and 20α-DHP, were far lower throughout pregnancy (<10 ng/ml). DHP and 3α-DHP decreased from early to mid-gestation in belugas, but changed little in killer whales and dolphins. These data suggest that progesterone metabolism is relatively conserved among these cetacean species. As in equine pregnancies, 3β,20α-DHP is the major metabolite, increasing at the expense of progesterone as pregnancy progresses. Androstenedione and testosterone also increased detectably in mid- to late-gestation in these species. The tissue source remains unknown, but progesterone metabolism during gestation in these cetaceans is similar to horses and, together with androgens, may be reliable biomarkers of pregnancy.

The Prevalence and Impact of Model Violations in Phylogenetic Analysis

In phylogenetic inference, we commonly use models of substitution which assume that sequence evolution is stationary, reversible, and homogeneous (SRH). Although the use of such models is often criticized, the extent of SRH violations and their effects on phylogenetic inference of tree topologies and edge lengths are not well understood. Here, we introduce and apply the maximal matched-pairs tests of homogeneity to assess the scale and impact of SRH model violations on 3,572 partitions from 35 published phylogenetic data sets. We show that roughly one-quarter of all the partitions we analyzed (23.5%) reject the SRH assumptions, and that for 25% of data sets, tree topologies inferred from all partitions differ significantly from topologies inferred using the subset of partitions that do not reject the SRH assumptions. This proportion increases when comparing trees inferred using the subset of partitions that rejects the SRH assumptions, to those inferred from partitions that do not reject the SRH assumptions. These results suggest that the extent and effects of model violation in phylogenetics may be substantial. They highlight the importance of testing for model violations and possibly excluding partitions that violate models prior to tree reconstruction. Our results also suggest that further effort in developing models that do not require SRH assumptions could lead to large improvements in the accuracy of phylogenomic inference. The scripts necessary to perform the analysis are available in https://github.com/roblanf/SRHtests, and the new tests we describe are available as a new option in IQ-TREE (http://www.iqtree.org).

Correlations between physiology and lifespan--two widely ignored problems with comparative studies

Comparative differences between species provide a powerful source of information that may inform our understanding of the aging process. However, two problems regularly attend such analyses. The co-variation of traits with body mass is frequently ignored, along with the lack of independence of the data due to a shared phylogenetic history. These problems undermine the use of simple correlations between various factors and maximum lifespan potential (MLSP) across different species as evidence that the factors in question have causal effects on aging. Both of these problems have been widely addressed by comparative biologists working in fields other than aging research, and statistical solutions to these issues are available. Using these statistical approaches, of making analyses of residual traits with the effects of body mass removed, and deriving phylogenetically independent contrasts, will allow analyses of the relationships between physiology and maximum lifespan potential to proceed unhindered by these difficulties, potentially leading to many useful insights into the aging process.

Orthologous repeats and mammalian phylogenetic inference

Determining phylogenetic relationships between species is a difficult problem, and many phylogenetic relationships remain unresolved, even among eutherian mammals. Repetitive elements provide excellent markers for phylogenetic analysis, because their mode of evolution is predominantly homoplasy-free and unidirectional. Historically, phylogenetic studies using repetitive elements have relied on biological methods such as PCR analysis, and computational inference is limited to a few isolated repeats. Here, we present a novel computational method for inferring phylogenetic relationships from partial sequence data using orthologous repeats. We apply our method to reconstructing the phylogeny of 28 mammals, using more than 1000 orthologous repeats obtained from sequence data available from the NISC Comparative Sequencing Program. The resulting phylogeny has robust bootstrap numbers, and broadly matches results from previous studies which were obtained using entirely different data and methods. In addition, we shed light on some of the debatable aspects of the phylogeny. With rapid expansion of available partial sequence data, computational analysis of repetitive elements holds great promise for the future of phylogenetic inference.

A memetic-aided approach to hierarchical clustering from distance matrices: application to gene expression clustering and phylogeny

We propose a heuristic approach to hierarchical clustering from distance matrices based on the use of memetic algorithms (MAs). By using MAs to solve some variants of the Minimum Weight Hamiltonian Path Problem on the input matrix, a sequence of the individual elements to be clustered (referred to as patterns) is first obtained. While this problem is also NP-hard, a probably optimal sequence is easy to find with the current advances for this problem and helps to prune the space of possible solutions and/or to guide the search performed by an actual clustering algorithm. This technique has been successfully applied to both a Branch-and-Bound algorithm, and to evolutionary algorithms and MAs. Experimental results are given in the context of phylogenetic inference and in the hierarchical clustering of gene expression data.

Model dependence of the phylogenetic inference: relationship among carnivores, Perissodactyls and cetartiodactyls as inferred from mitochondrial genome sequences

Some previous analysis of mitochondrial proteins strongly support the Carnivora/Perissodactyla grouping excluding Cetartiodactyla (Artiodactyla + Cetacea) as an outgroup, but the support of the hypothesis remains equivocal from the analysis of several nuclear-encoded proteins. In order to evaluate the strength of the support by mitochondrial proteins, phylogenetic relationship among Carnivora, Perissodactyla, and Cetartiodactyla was estimated with the ML method by using the updated data set of the 12 mitochondrial proteins with several alternative models. The analyses demonstrate that the phylogenetic inference depends on the model used in the ML analysis; i.e., whether the site-heterogeneity is taken into account and whether the rate parameters are estimated for each individual proteins or for the concatenated sequences. Although the analysis of concatenated sequences strongly supports the Carnivora/Perissodactyla grouping, the total evaluation of the separate analyses of individual proteins, which approximates the data better than the concatenated analysis, gives only ambiguous results, and therefore it is concluded that more data are needed to resolve this trichotomy.

Constructing phylogenies from quartets: elucidation of eutherian superordinal relationships

In this work we present two new approaches for constructing phylogenetic trees. The input is a list of weighted quartets over n taxa. Each quartet is a subtree on four taxa, and its weight represents a confidence level for the specific topology. The goal is to construct a binary tree with n leaves such that the total weight of the satisfied quartets is maximized (an NP hard problem). The first approach we present is based on geometric ideas. Using semidefinite programming, we embed the n points on the n-dimensional unit sphere, while maximizing an objective function. This function depends on Euclidean distances between the four points and reflects the quartet topology. Given the embedding, we construct a binary tree by performing geometric clustering. This process is similar to the traditional neighbor joining, with the difference that the update phase retains geometric meaning: When two neighbors are joined together, their common ancestor is taken to be the center of mass of the original points. The geometric algorithm runs in poly(n) time, but there are no guarantees on the quality of its output. In contrast, our second algorithm is based on dynamic programming, and it is guaranteed to find the optimal tree (with respect to the given quartets). Its running time is a modest exponential, so it can be implemented for modest values of n. We have implemented both algorithms and ran them on real data for n = 15 taxa (14 mammalian orders and an outgroup taxon). The two resulting trees improve previously published trees and seem to be of biological relevance. On this dataset, the geometric algorithm produced a tree whose score is 98.2% of the optimal value on this input set (72.1% vs. 73.4%). This gives rise to the hope that the geometric approach will prove viable even for larger cases where the exponential, dynamic programming approach is no longer feasible.

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.

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 interphotoreceptor retinoid binding protein gene in therian mammals: implications for higher level relationships and evidence for loss of function in the marsupial mole

The subclass Theria of Mammalia includes marsupials (infraclass Metatheria) and placentals (infraclass Eutheria). Within each group, interordinal relationships remain unclear. One limitation of many studies is incomplete ordinal representation. Here, we analyze DNA sequences for part of exon 1 of the interphotoreceptor retinoid binding protein gene, including 10 that are newly reported, for representatives of all therian orders. Among placentals, the most robust clades are Cetartiodactyla, Paenungulata, and an expanded African clade that includes paenungulates, tubulidentates, and macroscelideans. Anagalida, Archonta, Altungulata, Hyracoidea + Perissodactyla, Ungulata, and the "flying primate" hypothesis are rejected by statistical tests. Among marsupials, the most robust clade includes all orders except Didelphimorphia. The phylogenetic placement of the monito del monte and the marsupial mole remains unclear. However, the marsupial mole sequence contains three frameshift indels and numerous stop codons in all three reading frames. Given that the interphotoreceptor retinoid binding protein gene is a single-copy gene that functions in the visual cycle and that the marsupial mole is blind with degenerate eyes, this finding suggests that phenotypic degeneration of the eyes is accompanied by parallel changes at the molecular level as a result of relaxed selective constraints.