Stem Life: A Framework for Understanding the Prebiotic-Biotic Transition.

Abiogenesis is frequently envisioned as a linear, ladder-like progression of increasingly complex chemical systems, eventually leading to the ancestors of extant cellular life. This "pre-cladistics" view is in stark contrast to the well-accepted principles of organismal evolutionary biology, as informed by paleontology and phylogenetics. Applying this perspective to origins, I explore the paradigm of "Stem Life," which embeds abiogenesis within a broader continuity of diversification and extinction of both hereditary lineages and chemical systems. In this new paradigm, extant life's ancestral lineage emerged alongside and was dependent upon many other complex prebiotic chemical systems, as part of a diverse and fecund prebiosphere. Drawing from several natural history analogies, I show how this shift in perspective enriches our understanding of Origins and directly informs debates on defining Life, the emergence of the Last Universal Common Ancestor (LUCA), and the implications of prebiotic chemical experiments.

Description and molecular characterization of Trachactinolaimus persicus sp. n. from Iran (Nematoda, Dorylaimida, Actinolaimidae), with new insights into the taxonomy and evolutionary relationships of the genus.

A new species of the free-living nematode genus Trachactinolaimus, collected in natural habitats of northern Iran, is described, including morphological and molecular (28S-rDNA) data. Trachactinolaimus persicus sp. n. is characterized by its 1.95-2.44 mm long body, lip region weakly offset by depression and 18-20 µm wide, odontostyle 25-27 µm long, neck 540-636 µm long, pharyngeal expansion occupying one-half of the total neck length, bipartite uterus 2.6-3.9 body diameters long, vulva (V = 49-53) pore-like, tail long and filiform in both sexes (174-223 µm, c = 10.0-13.4, c' = 5.9-7.0 in females, 165-196 µm, c = 10.7-13.8, c' = 4.6-5.8 in males), spicules 68-75 µm long, and 12-14 almost contiguous ventromedian supplements with hiatus. Molecular data supports the monophyly of the genus and the hypothesis that Dorylaimidae are the sister group of actinolaims. The taxonomy of Trachactinolaimus is updated, including diagnosis, list of species, key to their identification, and a compendium of their main morphometrics. Dominiactinolaimus is regarded as its junior synonym.

Two new species of the genus Sectonema Thorne, 1930 (Nematoda, Dorylaimida, Aporcelaimidae) from Iran, with new insights into its evolutionary relationships.

Two new species of the genus Sectonema found in northern Iran are characterized, including morphological descriptions and molecular (18S-, 28S-rDNA) analyses. Sectonema tehranense sp. nov. is distinguished by its 7.22 - 8.53 mm long body, lip region offset by constriction and 24 - 31 µm wide with perioral lobes and abundant setae- or cilia-like projections covering the oral field, mural tooth 15.5 - 17 µm long at its ventral side, neck 1091 - 1478 µm long, pharyngeal expansion occupying 61 - 71% of the total neck length, female genital system diovarian, uterus simple and 3.9 - 4.2 times the corresponding body diameter long, transverse vulva (V = 49 - 59), tail short and rounded (44 - 65 µm, c = 99 - 162, c' = 0.6 - 0.8), spicules 111 - 127 µm long, and 7 - 10 spaced ventromedian supplements with hiatus. Sectonema noshahrense sp. nov. displays a 4.07 - 4.73 mm long body, lip region offset by constriction and 23 - 25 µm wide with perioral lobes and abundant setae- or cilia-like projections covering the oral field, odontostyle 14 - 14.5 µm long, neck 722 - 822 µm long, pharyngeal expansion occupying 66 - 68% of the total neck length, female genital system diovarian, uterus simple and 2.4 - 2.7 times the corresponding body diameter long, transverse vulva (V = 54 - 55), tail convex conoid (39 - 47 µm, c = 91 - 111, c' = 0.8 - 0.9), spicules 82 µm long, and seven spaced ventromedian supplements with hiatus. Molecular analyses confirm a maximally supported (Epacrolaimus + Metaporcelaimus + Sectonema) clade and a tentative biogeographical pattern, with sequences of Indolamayan taxa forming a clade separated from those of Palearctic ones. Parallel or convergent evolution processes might be involved in the phylogeny of the species currently classified under Sectonema. This genus is certainly more heterogeneous than previously assumed.

Implications of outgroup selection in the phylogenetic inference of hominoids and fossil hominins.

Understanding the phylogenetic relationships among hominins and other hominoid species is critical to the study of human origins. However, phylogenetic inferences are dependent on both the character data and taxon sampling used. Previous studies of hominin phylogenetics have used Papio and Colobus as outgroups in their analyses; however, these extant monkeys possess many derived traits that may confound the polarities of morphological changes among living apes and hominins. Here, we consider Victoriapithecus and Ekembo as more suitable outgroups. Both Victoriapithecus and Ekembo are anatomically well known and are widely accepted as morphologically primitive stem cercopithecoid and hominoid taxa, respectively, making them more appropriate for inferring polarity for later-occurring hominoid- and hominin-focused analyses. Craniodental characters for both taxa were scored and then added to a previously published matrix of fossil hominin and extant hominoid taxa, replacing outgroups Papio and Colobus over a series of iterative analyses using both parsimony and Bayesian inference methods. Neither the addition nor replacement of outgroup taxa changed tree topology in any analysis. Importantly, however, bootstrap support values and posterior probabilities for nodes supporting their relationships generally increased compared to previous analyses. These increases were the highest at extant hominoid and basal hominin nodes, recovering the molecular ape phylogeny with considerably higher support and strengthening the inferred relationships among basal hominins. Interestingly, however, the inclusion of both extant and fossil outgroups reduced support for the crown hominid node. Our findings suggest that, in addition to improving character polarity estimation, including fossil outgroups generally strengthens confidence in relationships among extant hominoid and basal hominins.

Systematics of Miocene apes: State of the art of a neverending controversy.

Hominoids diverged from cercopithecoids during the Oligocene in Afro-Arabia, initially radiating in that continent and subsequently dispersing into Eurasia. From the Late Miocene onward, the geographic range of hominoids progressively shrank, except for hominins, which dispersed out of Africa during the Pleistocene. Although the overall picture of hominoid evolution is clear based on available fossil evidence, many uncertainties persist regarding the phylogeny and paleobiogeography of Miocene apes (nonhominin hominoids), owing to their sparse record, pervasive homoplasy, and the decimated current diversity of this group. We review Miocene ape systematics and evolution by focusing on the most parsimonious cladograms published during the last decade. First, we provide a historical account of the progress made in Miocene ape phylogeny and paleobiogeography, report an updated classification of Miocene apes, and provide a list of Miocene ape species-locality occurrences together with an analysis of their paleobiodiversity dynamics. Second, we discuss various critical issues of Miocene ape phylogeny and paleobiogeography (hylobatid and crown hominid origins, plus the relationships of Oreopithecus) in the light of the highly divergent results obtained from cladistic analyses of craniodental and postcranial characters separately. We conclude that cladistic efforts to disentangle Miocene ape phylogeny are potentially biased by a long-branch attraction problem caused by the numerous postcranial similarities shared between hylobatids and hominids-despite the increasingly held view that they are likely homoplastic to a large extent, as illustrated by Sivapithecus and Pierolapithecus-and further aggravated by abundant missing data owing to incomplete preservation. Finally, we argue that-besides the recovery of additional fossils, the retrieval of paleoproteomic data, and a better integration between cladistics and geometric morphometrics-Miocene ape phylogenetics should take advantage of total-evidence (tip-dating) Bayesian methods of phylogenetic inference combining morphologic, molecular, and chronostratigraphic data. This would hopefully help ascertain whether hylobatid divergence was more basal than currently supported.

A new approach to exploratory data analysis in hominin phylogenetic reconstruction.

The phylogenetic relationships between fossil hominin taxa have been a contentious topic for decades. Recent discoveries of new taxa, rather than resolving the issue, have only further confused it. Compounding this problem are the limitations of some of the tools frequently used by paleoanthropologists to analyze these relationships. Most commonly, phylogenetic questions are investigated using analytical methods such as maximum parsimony and Bayesian analysis. While these are useful analytical tools, these tree-building methods can have limitations when investigating taxa that may have complex evolutionary histories. Exploratory data analysis can provide information about patterns in a dataset that are obscured by tree-based methods. These patterns include phylogenetic signal conflict, which is not depicted in tree-based methods. Signal conflict can have a number of sources, including methodological issues with character choice, taxonomic issues, homoplasy, and gene flow between taxa. In this study, an exploratory data analysis of fossil hominin morphological data is conducted using the tree-based analytical method neighbor-joining and the network-based analytical method neighbor-net with the goal of visualizing phylogenetic signal conflict within a hominin morphological data set. The data set is divided into cranial regions, and each cranial region is analyzed individually to investigate which regions of the skull contain the highest levels of signal conflict. Results of this analysis show that conflicting phylogenetic signals are present in the hominin fossil record during the relatively speciose period between 3 and 1 Ma, and they also indicate that levels of signal conflict vary by cranial region. Possible sources of these conflicting signals are then explored. Exploratory data analyses such as this can be a useful tool in generating phylogenetic hypotheses and in refining character choice. This study also highlights the value network-based approaches can bring to the hominin phylogenetic analysis toolkit.

Evolution of Local Circuit Neurons in Two Sensory Thalamic Nuclei in Amniotes.

Local circuit neurons are present in the thalamus of all vertebrates where they are considered inhibitory. They play an important role in computation and influence the transmission of information from the thalamus to the telencephalon. In mammals, the percentage of local circuit neurons in the dorsal lateral geniculate nucleus remains relatively constant across a variety of species. In contrast, the numbers of local circuit neurons in the ventral division of the medial geniculate body in mammals vary significantly depending on the species examined. To explain these observations, the numbers of local circuit neurons were investigated by reviewing the literature on this subject in these two nuclei in mammals and their respective homologs in sauropsids and by providing additional data on a crocodilian. Local circuit neurons are present in the dorsal geniculate nucleus of sauropsids just as is the case for this nucleus in mammals. However, sauropsids lack local circuits neurons in the auditory thalamic nuclei homologous to the ventral division of the medial geniculate body. A cladistic analysis of these results suggests that differences in the numbers of local circuit neurons in the dorsal lateral geniculate nucleus of amniotes reflect an elaboration of these local circuit neurons as a result of evolution from a common ancestor. In contrast, the numbers of local circuit neurons in the ventral division of the medial geniculate body changed independently in several mammalian lineages.

On Pattern-Cladistic Analyses Based on Complete Plastid Genome Sequences.

The fundamental Hennigian principle, grouping solely on synapomorphy, is seldom used in modern phylogenetics. In the submitted paper, we apply this principle in reanalyzing five datasets comprising 197 complete plastid genomes (plastomes). We focused on the latter because plastome-based DNA sequence data gained dramatic popularity in molecular systematics during the last decade. We show that pattern-cladistic analyses based on complete plastid genome sequences can successfully resolve affinities between plant taxa, simultaneously simplifying both the genomic and analytical frameworks of phylogenetic studies. We developed "Matrix to Newick" (M2N), a program to represent the standard molecular alignment of plastid genomes in the form of trees or relationships directly. Thus, massive plastome-based DNA sequence data can be successfully represented in a relational form rather than as a standard molecular alignment. Application of methods of median supertree construction (the Average Consensus method has been used as an example in this study) or Maximum Parsimony analysis to relational representations of plastome sequence data may help systematist to avoid the complicated assumption-based frameworks of Maximum Likelihood or Bayesian phylogenetics that are most used today in massive plastid sequence data analyses. We also found that significant amounts of pure genomic information that typically accommodate the majority of current plastid phylogenomic studies can be effectively dropped by systematists if they focus on the pattern-cladistics or relational analyses of plastome-based molecular data. The proposed pattern-cladistic approach is a powerful and straightforward heuristic alternative to modern plastome-based phylogenetics.

The enigmatic genus Loofilaimus (Nematoda, Dorylaimida, Loofilaimidae) revisited 25 years after, with remarkable new insights into its phylogeny.

The evolutionary relationships of the nematode genus Loofilaimus are explored with an integrative approach, combining morphological and molecular (28S-rDNA) data. Never recorded since its original description in 1998, the finding of fresh specimens of its type and only species, L. phialistoma, allowed us to obtain SEM observations and sequencing, both for the first time, resulting in relevant aspects to elucidate its phylogeny. Morphologically, the genus is characterized by two autapomorphies affecting its lip region and pharynx. Molecular study revealed that it represents a very restricted evolutionary trend within Dorylaimida. The clade (Nygolaimina + (Loofilaimus + Dorylaimina)) is well supported. Loofilaimidae is accepted as a separate and valid family, which should also include Bertzuckermania.

Phylogenetic analysis of Middle-Late Miocene apes.

Despite intensive study, many aspects of the evolutionary history of great apes and humans (Hominidae) are not well understood. In particular, the phylogenetic relationships of many fossil taxa remain poorly resolved. This study aims to provide an updated hypothesis of phylogenetic relationships for Middle-Late Miocene fossil apes, focusing on those taxa typically considered to be great apes. The character matrix compiled here samples 274 characters from the skull, dentition, and postcranium. Multiple iterations were performed to examine the effects of ingroup taxon selection, outgroup constraints, treatment of continuous data, character partitions (craniodental, postcranial), and missing data. Parsimony and Bayesian methods were used to infer phylogenetic relationships. Most European hominoids (Hispanopithecus, Rudapithecus, Dryopithecus, Pierolapithecus) are recovered as stem hominids, not more closely related to orangutans or to African apes and humans (Homininae), whereas Ouranopithecus, Graecopithecus, and Nakalipithecus are inferred to be members of the hominine clade. Asian fossil hominoids, with the exception of Lufengpithecus hudienensis, are recovered as part of the orangutan clade (Ponginae). Results suggest that Kenyapithecus and Griphopithecus are possible stem hominids, whereas Equatorius and Nacholapithecus are consistently recovered as stem hominoids. Oreopithecus and Samburupithecus are not recovered as hominids. Results of Bayesian analyses differ from those of parsimony analyses. Craniodental and postcranial character partitions are incongruent in the placement of hylobatids, which is interpreted as evidence that hylobatids and hominids independently evolved adaptations to suspensory positional behaviors. An understanding of phylogenetic relationships is necessary to address many of the questions asked in paleoanthropology. Thus, the updated hypothesis of phylogenetic relationships presented here can be used to gain a better understanding of important morphological transitions that took place during hominid evolution, ancestral morphotypes at key nodes, and the biogeography of the clade.

Origins and spread of fluted-point technology in the Canadian Ice-Free Corridor and eastern Beringia.

Fluted projectile points have long been recognized as the archaeological signature of early humans dispersing throughout the Western Hemisphere; however, we still lack a clear understanding of their appearance in the interior "Ice-Free Corridor" of western Canada and eastern Beringia. To solve this problem, we conducted a geometric morphometric shape analysis and a phylogenetic analysis of technological traits on fluted points from the archaeological records of northern Alaska and Yukon, in combination with artifacts from further south in Canada, the Great Plains, and eastern United States to investigate the plausibility of historical relatedness and evolutionary patterns in the spread of fluted-point technology in the latest Pleistocene and earliest Holocene. Results link morphologies and technologies of Clovis, certain western Canadian, and northern fluted points, suggesting that fluting technology arrived in the Arctic from a proximate source in the interior Ice-Free Corridor and ultimately from the earliest populations in temperate North America, complementing new genomic models explaining the peopling of the Americas.

Synapomorphies Behind Shared Derived Characters: Examples from the Great Apes' Genomic Data.

Phylogenetic systematics (e.g., cladistics) is one of the most important analytical frameworks of modern Biology. It seems to be common knowledge that within phylogenetics, 'groups' must be defined based solely on the synapomorphies or on the "derived" characters that unite two or more taxa in a clade or monophyletic group. Thus, the idea of synapomorphy seems to be of fundamental influence and importance. Here I will show that the most common and straightforward understanding of synapomorphy as a shared derived character is not sufficient and eventually must be rejected in favor of Nelson's relational interpretation of such term. Arguing for this point and using three examples from previously published Apes' genomic matrices, I explicitly demonstrate that the relationship (Pongo (Gorilla (Homo, Pan))) with Hylobatidae as a sister taxon, may be successfully recovered by three-taxon statement analysis (3TA) and three-taxon statement average consensus analysis (3TS-ACA) even if all of the evident standard shared derived molecular characters of the relationship (Pongo (Gorilla (Homo, Pan))) with Hylobatidae as a sister taxon, have been excluded from the molecular alignments. Neither conventional Maximum Parsimony nor Maximum Likelihood or Bayesian Inference can do this in such situation. Thus, our results show that the relationship (Pongo (Gorilla (Homo, Pan))) with Hylobatidae as a sister taxon has appeared, in some way, behind standard shared derived characters: the last ones could be excluded, but the relationship remains the same.

Expanded character sampling underscores phylogenetic stability of Ardipithecus ramidus as a basal hominin.

Phylogenetic relationships among hominins provide a necessary framework for assessing their evolution. Reconstructing these relationships hinges on the strength of the character data analyzed. The phylogenetic position of Ardipithecus ramidus is critical to understanding early hominin evolution, and while many accept that it is most likely the sister taxon to all later hominins, others have argued that Ar. ramidus was ancestral to Pan. Although the study by Strait and Grine (2004) suggested the former, available evidence permitted only 26% of characters in their matrix to be assessed for Ar. ramidus. Fossils described subsequently by Suwa, White and colleagues in 2009 have enabled the number of characters that can be coded for this species to be expanded to 78% of the matrix. Here, we incorporate these new character data to evaluate their impact on the phylogenetic relationships of Ar. ramidus. Moreover, we have further revised the Strait and Grine (2004) matrix as necessitated by additions to the hypodigms of other fossil taxa. This updated matrix was analyzed using both parsimony and Bayesian techniques in a sequence of four iterative steps to independently evaluate the impact of matrix and expanded character revisions on tree topology. Despite the new data and matrix revisions, tree topology has remained remarkably stable. The addition of new craniodental material has served to markedly strengthen the support for the placement of Ar. ramidus as being derived relative to Sahelanthropus, and as the sister taxon of all later hominins. These findings support the phylogenetic hypothesis originally proposed by White and colleagues in 1994. This updated matrix provides a basis for the assessment of additional extinct species.

Phylogeny, new generic-level classification, and historical biogeography of the Eucera complex (Hymenoptera: Apidae).

The longhorn bee tribe Eucerini (Hymenoptera: Apidae) is a diverse, widely distributed group of solitary bees that includes important pollinators of both wild and agricultural plants. About half of the species in the tribe are currently assigned to the genus Eucera and to a few other related genera. In this large genus complex, comprising ca. 390 species, the boundaries between genera remain ambiguous due to morphological intergradation among taxa. Using ca. 6700 aligned nucleotide sites from six gene fragments, 120 morphological characters, and more than 100 taxa, we present the first comprehensive molecular, morphological, and combined phylogenetic analyses of the 'Eucera complex'. The revised generic classification that we propose is congruent with our phylogeny and maximizes both generic stability and ease of identification. Under this new classification most generic names are synonymized under an expanded genus Eucera. Thus, Tetralonia, Peponapis, Xenoglossa, Cemolobus, and Syntrichalonia are reduced to subgeneric rank within Eucera, and Synhalonia is retained as a subgenus of Eucera. Xenoglossodes is reestablished as a valid subgenus of Eucera while Tetraloniella is synonymized with Tetralonia and Cubitalia with Eucera. In contrast, we suggest that the venusta-group of species, currently placed in the subgenus Synhalonia, should be recognized as a new genus. Our results demonstrate the need to evaluate convergent loss or gain of important diagnostic traits to minimize the use of potentially homoplasious characters when establishing classifications. Lastly, we show that the Eucera complex originated in the Nearctic region in the late Oligocene, and dispersed twice into the Old World. The first dispersal event likely occurred 24.2-16.6 mya at a base of a clade of summer-active bees restricted to warm region of the Old World, and the second 13.9-12.3 mya at the base of a clade of spring-active bees found in cooler regions of the Holarctic. Our results further highlight the role of Beringia as a climate-regulated corridor for bees.

Ontogenetic Data Analyzed As Such in Phylogenies.

Ontogeny is rarely included in phylogenetic analyses of morphological data. When used, the ontogenetic information is reduced to one character for two or three different ontogenetic stages. Several examples show that current methods miss a major part of the information. We here propose a new method for including the ontogenetic dimension in coding schemes of phylogenetic analyses. Our goal was to maximize the phylogenetic information extracted from ontogenetic trajectories. For discrete features, we recommend including precise timings of transformation(s) from one state to another in the ontogenetic trajectories. For continuously varying features, growth laws are modeled on raw data using least-square regressions. Then, parameters of models are included in the coding scheme as continuous characters. This method is employed to reconstruct phylogenetic relationships using the ammonite family Amaltheidae as a test subject. Based on the same data set, a second analysis has been performed only for characters of the adult stage. Comparisons of retention index, bootstrap support, and stratigraphic congruence between the two analyses show that the inclusion of ontogeny yields better phylogenetic reconstruction. Morphological traits in ammonites which are usually the most homoplastic show a better fit to most parsimonious trees by including the ontogenetic dimension. In several cases, growth rates and patterns of growth have better fit to phylogeny than adult shapes, implying that paths of ontogeny can be more relevant than its products.

Origin of Equisetum: Evolution of horsetails (Equisetales) within the major euphyllophyte clade Sphenopsida.

PREMISE OF THE STUDY: Equisetum is the sole living representative of Sphenopsida, a clade with impressive species richness, a long fossil history dating back to the Devonian, and obscure relationships with other living pteridophytes. Based on molecular data, the crown group age of Equisetum is mid-Paleogene, although fossils with possible crown synapomorphies appear in the Triassic. The most widely circulated hypothesis states that the lineage of Equisetum derives from calamitaceans, but no comprehensive phylogenetic studies support the claim. Using a combined approach, we provide a comprehensive phylogenetic analysis of Equisetales, with special emphasis on the origin of genus Equisetum. METHODS: We performed parsimony phylogenetic analyses to address relationships of 43 equisetalean species (15 extant, 28 extinct) using a combination of morphological and molecular characters. KEY RESULTS: We recovered Equisetaceae + Neocalamites as sister to Calamitaceae + a clade of Angaran and Gondwanan horsetails, with the four groups forming a clade that is sister to Archaeocalamitaceae. The estimated age for the Equisetum crown group is mid-Mesozoic. CONCLUSIONS: Modern horsetails are not nested within calamitaceans; instead, both groups have explored independent evolutionary trajectories since the Carboniferous. Diverse fossil taxon sampling helps to shed light on the position and relationships of equisetalean lineages, of which only a tiny remnant is present within the extant flora. Understanding these relationships and early character configurations of ancient plant clades as Equisetales provide useful tests of hypotheses about overall phylogenetic relationships of euphyllophytes and foundations for future tests of molecular dates with paleontological data.

A sort of revolution: Systematics and physical anthropology in the 20th century.

During the first four decades of the 20th century, a system of ideas about the evolution and systematics of humans and other primates coalesced around the work of George Gaylord Simpson and W. E. Le Gros Clark. Buttressed by the "new physical anthropology" of the 1950s, that system provided an authoritative model-a disciplinary matrix or paradigm-for the practice of that aspect of biological anthropology. The Simpson-Le Gros Clark synthesis began to unravel in the 1960s and collapsed in the 1970s under the onslaught of cladistic systematics. The cladistic "revolution" resembles a paradigm shift of the sort proposed by Thomas Kuhn because it was driven, not by new biological discoveries or theories, but by a change in aesthetics.

Moving Past the Systematics Wars.

It is time to escape the constraints of the Systematics Wars narrative and pursue new questions that are better positioned to establish the relevance of the field in this time period to broader issues in the history of biology and history of science. To date, the underlying assumptions of the Systematics Wars narrative have led historians to prioritize theory over practice and the conflicts of a few leading theorists over the less-polarized interactions of systematists at large. We show how shifting to a practice-oriented view of methodology, centered on the trajectory of mathematization in systematics, demonstrates problems with the common view that one camp (cladistics) straightforwardly "won" over the other (phenetics). In particular, we critique David Hull's historical account in Science as a Process by demonstrating exactly the sort of intermediate level of positive sharing between phenetic and cladistic theories that undermines their mutually exclusive individuality as conceptual systems over time. It is misleading, or at least inadequate, to treat them simply as holistically opposed theories that can only interact by competition to the death. Looking to the future, we suggest that the concept of workflow provides an important new perspective on the history of mathematization and computerization in biology after World War II.

Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data.

Morphological data provide the only means of classifying the majority of life's history, but the choice between competing phylogenetic methods for the analysis of morphology is unclear. Traditionally, parsimony methods have been favoured but recent studies have shown that these approaches are less accurate than the Bayesian implementation of the Mk model. Here we expand on these findings in several ways: we assess the impact of tree shape and maximum-likelihood estimation using the Mk model, as well as analysing data composed of both binary and multistate characters. We find that all methods struggle to correctly resolve deep clades within asymmetric trees, and when analysing small character matrices. The Bayesian Mk model is the most accurate method for estimating topology, but with lower resolution than other methods. Equal weights parsimony is more accurate than implied weights parsimony, and maximum-likelihood estimation using the Mk model is the least accurate method. We conclude that the Bayesian implementation of the Mk model should be the default method for phylogenetic estimation from phenotype datasets, and we explore the implications of our simulations in reanalysing several empirical morphological character matrices. A consequence of our finding is that high levels of resolution or the ability to classify species or groups with much confidence should not be expected when using small datasets. It is now necessary to depart from the traditional parsimony paradigms of constructing character matrices, towards datasets constructed explicitly for Bayesian methods.

HIV migration between blood plasma and cellular subsets before and after HIV therapy.

The cellular source of HIV RNA circulating in blood plasma remains unclear. Here, we investigated whether sequence analysis of HIV RNA populations circulating before combination antiretroviral therapy (cART) and HIV DNA populations in cellular subsets (CS) after cART could identify the cellular sources of circulating HIV RNA. Blood was collected from five subjects at cART initiation and again 6 months later. Naïve CD4+ T cells, resting central memory and effector memory CD4+ T cells, activated CD4+ T cells, monocytes, and natural killer cells were sorted using a fluorescence-activated cell sorter. HIV-1 env C2V3 sequences from HIV RNA in blood plasma and HIV DNA in CSs were generated using single genome sequencing. Sequences were evaluated for viral compartmentalization (Fst test) and migration events (MEs; Slatkin Maddison and cladistic measures) between blood plasma and each CS. Viral compartmentalization was observed in 88% of all cellular subset comparisons (range: 77-100% for each subject). Most observed MEs were directed from blood plasma to CSs (52 MEs, 85.2%). In particular, there was only viral movement from plasma to NK cells (15 MEs), monocytes (seven MEs), and naïve cells (five ME). We observed a total of nine MEs from activated CD4 cells (2/9 MEs), central memory T cells (3/9 MEs), and effector memory T cells (4/9 MEs) to blood plasma. Our results revealed that the HIV RNA population in blood plasma plays an important role in seeding various cellular reservoirs and that the cellular source of the HIV RNA population is activated central memory and effector memory T cells.