STATISTICAL COVARIANCE AS A MEASURE OF PHYLOGENETIC RELATIONSHIP

Abstract— The method of parsimony in phylogenetic inference is often taken to mean two things: (1) that one should favor the genealogical hypothesis that minimizes the required number of homoplasies ( matchings of independently evolved derived character states ), and (2) that symplesiomorphies (matchings of primitive character states) have little or no evidential value for phylogenetic relationship. This paper shows both theses to be false by undermining recent likelihood arguments for them and by providing a more secure likelihood proof of a new method, which is incompatible with both (1) and (2).     

Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches: a case study using mitogenomic data from 100 higher teleost fishes

Many phylogenetic analyses that include numerous terminals but few genes show high resolution and branch support for relatively recently diverged clades, but lack of resolution and/or support for "basal" clades of the tree. The various benefits of increased taxon and character sampling have been widely discussed in the literature, albeit primarily based on simulations rather than empirical data. In this study, we used a well-sampled gene-tree analysis (based on 100 mitochondrial genomes of higher teleost fishes) to test empirically the efficiency of different methods of data sampling and phylogenetic inference to "correctly" resolve the basal clades of a tree (based on congruence with the reference tree constructed using all 100 taxa and 7990 characters). By itself, increased character sampling was an inefficient method by which to decrease the likelihood of "incorrect" resolution (i.e., incongruence with the reference tree) for parsimony analyses. Although increased taxon sampling was a powerful approach to alleviate "incorrect" resolution for parsimony analyses, it had the general effect of increasing the number of, and support for, "incorrectly" resolved clades in the Bayesian analyses. For both the parsimony and Bayesian analyses, increased taxon sampling, by itself, was insufficient to help resolve the basal clades, making this sampling strategy ineffective for that purpose. For this empirical study, the most efficient of the six approaches considered to resolve the basal clades when adding nucleotides to a dataset that consists of a single gene sampled for a small, but representative, number of taxa, is to increase character sampling and analyze the characters using the Bayesian method.     

A Review of Current Theories and Methods in Cladistics and a Cladistic Study of Twelve Lindera Species in Eastern China

Cladistics has become a widely used method for phylogenetic reconstruction．Because of rapid improvement Of cladistic theories and methodologies,and application of new data,especially,molecular data,it is becoming realistic to reconstruct phylogenies of organisms,and to establish natural classifications based on these phylogenies．This paper reviews some current cladistic theories and methods in a practical way,such as choosing characters,defining character states,polarizing characters,analyzing data matrices, calculating consensus cladograms,choosing among multiple equally most parsimonious cladograms,estimating reliability of cladograms,and applying cladograms to classification, character evolution,and biogeography． Based on 36 morphological characters．a parsimony analysis of 12 species representing six sections in subgenus Lindera and an outgroup species from subgenus lteodaphne of the genus Lindera(Lauraceae)was conducted．The results suggest a close relationship between section Lindera and section Sphaerocarpae,which is different from the previous phylogenetic hypothesis within the genus．In the strict consensus cladogram,two species,L．megaphylla and L.chienii,from section Cupuliformes are in the most primitive and the most advanced clades respectively,indicating that the section is polyphyletic．The cladogram also suggests that section Lindera be a polyphyletic group．     

The evolution of the Proteocephalidea (Platyhelminthes,Eucestoda) based on an enlarged molecular phylogeny,with comments on their uterine development

We present a molecular phylogeny of the Proteocephalidea based on 28S rDNA sequence data that is a follow-up to the paper by Zehnder & Mariaux (1999). Twenty-three new sequences, including three outgroups are added in our new data-set. The Gangesiinae Mola, 1929 and the Acanthotaeniinae Freze, 1963 appear to be the most primitive clades. They are followed by a robust clade comprising the Palaearctic Proteocephalinae Mola, 1929 from freshwater fishes. The structure of the more derived clades, comprising most Neotropical and Nearctic species, is less resolved. At the nomenclatural level, we erect a new genus, Glanitaenia n. g. for G. osculata (Goeze, 1782) n. comb., previously Proteocephalus osculatus, and define an aggregate for the Palaearctic Proteocephalus Weinland, 1858. After a re-examination of all of the studied taxa, we identify two types of uterine development and show the importance of this character for the systematics of the order. Our phylogeny does not support the classical view of a Neotropical origin for the Proteocephalidea but rather favours an Old World origin of the group either in saurians or Palaearctic Siluriformes.     

Why a right to life rules out infanticide: A final reply to Räsänen

Joona Räsänen has argued that pro‐life arguments against the permissibility of infanticide are not persuasive, and fail to show it to be immoral. We responded to Räsänen’s arguments, concluding that his critique of pro‐life arguments was misplaced. Räsänen has recently replied in ‘Why pro‐life arguments still are not convincing: A reply to my critics’, providing some additional arguments as to why he does not find pro‐life arguments against infanticide convincing. Here, we respond briefly to Räsänen’s critique of the substance view, and also to his most important claim: that possession of a right to life by an infant does not rule out the permissibility of infanticide. We demonstrate that this claim is unfounded, and conclude that Räsänen has not refuted pro‐life arguments against infanticide.     

Exhaustion of morphologic character states among fossil taxa

Frequencies of new character state derivations are analyzed for 56 fossil taxa. The hypothesis that new character states are added continuously throughout clade history can be rejected for 48 of these clades. Two alternative explanations are considered: finite states and ordered states. The former hypothesizes a limited number of states available to each character and is tested using rarefaction equations. The latter hypothesizes that there are limited possible descendant morphologies for any state, even if the character has infinite potential states. This is tested using power functions. The finite states hypothesis explains states: steps relationships significantly better than does the ordered states hypothesis in 14 cases; the converse is true for 14 other cases. Under either hypothesis, trilobite clades show appreciably more homoplasty after the same numbers of steps than do molluscs, echinoderms, or vertebrates. The prevalence of the exhaustion pattern among different taxonomic groups implies that worker biases are not to blame and instead implicates biological explanations such as intrinsic constraints or persistent selective trends. Regardless of the source of increased homoplasy, clades appear to exhaust their available character spaces. Nearly all examined taxa show significant increases in proportions of incompatible character pairs (i.e., those necessarily implying homoplasy) as progressively younger taxa are added to character matrices. Thus, a deterioration of hierarchical structure accompanies character state exhaustion. Exhaustion has several implications: (1) the basic premise of cladistic analyses (i.e., that maximum congruence reflects homology rather than homoplasy) becomes increasingly less sound as clades age; (2) sampling high proportions of taxa probably is needed for congruence to discern homoplasy from homology; (3) stratigraphic data might be necessary to discern congruent homoplasy from congruent homology; and (4) in many cases, character states appear to have evolved in ordered patterns.     

Genetic diversity and the biogeographical process of Acheilognathus macropterus revealed by sequence variations of mitochondrial cytochrome b gene

In this study, thirty-six individuals of Acheilognathus macropterus were collected from the Heilongjiang River,the Yangtze River,and the Nandujiang River.Partial mitochondrial cytochrome b gene region (636 base pair) was sequenced to these samples and 22 haplotypes were found.With A.chankaensis and A.tokinensis as outgroups,their relationships were analyzed.The p-distances were calculated with Mega software and a molecular phyiogenetic tree was constructed using the neighbor-joining (NJ) method.The proportions of main morphological characters were compared as well.P-distances showed that the genetic differences in A.macropterus samples were far smaller than those between these samples and the outgroups.The molecular phylogenetic tree shows that samples with barbels and those without barbels were intermingled.There was no distinctive difference in proportions of morphological characteristics among them.These results suggested that samples with barbels and those without barbels (formally identified as A.taenianalis) are the same species;A.taenianalis is synonymous with A.macropterus.The thirtysix individuals were grouped into five clades and the positions of the samples in the clades were correspondingly grouped within their geographical distributions.Among the five clades,clades 1 and 5 included samples from the Heilongjiang River and Nandujiang River respectively.The samples from the Yangtze River scattered into clades 2,3,and 4.There were distinctive genetic differences (> 5%)among them.Interestingly,the distributions of the 21 samples in these three clades were not correlated to their geographical distributions.It is postulated that these genetic differences were due to the bitterlings' mating choice mechanism,the prozygotic isolation.The genetic differences between the fish from Nandujiang River and those from the mainland indicated that they were separated early.However,the small genetic differences among the samples and the positions of the fish from the Heilonjiang River in the molecular phylogenetic tree indicate that fish in Heilongjiang River might have dispersed from the Yangtze River to that area much later.     

The tree of life and the rock of ages: Are we getting better at estimating phylogeny?

In a recent paper,(1) palaeontologist Mike Benton claimed that our ability to reconstruct accurately the tree of Life may not have improved significantly over the last 100 years. This implies that the cladistic and molecular revolutions may have promulgated as much bad "black box" science as rigorous investigation. Benton's assessment was based on the extent to which cladograms (typically constructed with reference only to distributions of character states) convey the same narrative as the geochronological ages of fossil taxa (an independent data set). Fossil record quality varies greatly between major clades, and the palaeontological dating "yardstick" may be more appropriate for some groups than others.     

Variation, variability, and the origin of the avian endocranium: insights from the anatomy of Alioramus altai (Theropoda: Tyrannosauroidea)

The internal braincase anatomy of the holotype of Alioramus altai, a relatively small-bodied tyrannosauroid from the Late Cretaceous of Mongolia, was studied using high-resolution computed tomography. A number of derived characters strengthen the diagnosis of this taxon as both a tyrannosauroid and a unique, new species (e.g., endocranial position of the gasserian ganglion, internal ramification of the facial nerve). Also present are features intermediate between the basal theropod and avialan conditions that optimize as the ancestral condition for Coelurosauria--a diverse group of derived theropods that includes modern birds. The expression of several primitive theropod features as derived character states within Tyrannosauroidea establishes previously unrecognized evolutionary complexity and morphological plasticity at the base of Coelurosauria. It also demonstrates the critical role heterochrony may have played in driving patterns of endocranial variability within the group and potentially reveals stages in the evolution of neuroanatomical development that could not be inferred based solely on developmental observations of the major archosaurian crown clades. We discuss the integration of paleontology with variability studies, especially as applied to the nature of morphological transformations along the phylogenetically long branches that tend to separate the crown clades of major vertebrate groups.     

大鳍鱊基于细胞色素b基因序列的遗传变异及生物地理过程

对采集于长江水系、黑龙江水系及海南岛的36尾大鳍(Acheilognathus macropterus)的细胞色素b基因序列进行了研究分析。发现有须个体和无须个体在分子系统树中处于混合分布状态,各个体相互间遗传变异远小于与外类群(A.chankaensis、A.tokinensis)间差异,统计了其主要形态度量数据,也显示各主要性状数据无显著差异,结果均支持有须个体和无须个体(曾经被鉴定为A.taenianalis)为同一物种,A.taenianalis为A.macropterus的同物异名。序列分析显示,36个个体明显聚合成5个大的分支,其中clade1分支全部由黑龙江水系类群组成,clade5分支由海南岛的1个个体组成,长江水系的所有个体分散在clade2、clade3、clade4这三个分支中,显示出一定的地理相关性。在clade2、3、4中,clade2包括了长江上游的5个个体和长江中游的2个个体,同时还包括了黑龙江的2个个体;clade3包括了中游的2个个体;clade4包括了中游的12个个体,三个分支间又存在明显的遗传变异率(均>5%),从21个个体在三个分支中的分布情况来看,三者间这种较大的遗传变异率不能由地理隔离解释,故推测,造成同一水系的A.macropterus间出现较明显遗传分化的原因可能与其特殊的性选择生殖方式有关,该生殖方式限制了不同生殖集群间同种鱼类的基因交流。基于系统分支图,计算了各分支间的遗传距离,由结果推测大鳍的生物地理过程为:海南岛水系类群同大陆类群较早产生隔离,黑龙江水系类群由长江水系类群在晚近时期向北扩散形成。       

A subordinal classification of frogs (Amphibia: Anura)

Two new anuran suborders, based on two states of the trigeminofacial ganglion character complex are proposed. A subsidiary character is the presence or absence of free ribs in extant taxa. These new suborders are more clades (sister groups) than sequential levels of organization. Discoglossoidei, retaining separate trigeminal and facial ganglia and free ribs, encompasses only Leiopelmatidae and Discoglossidae, although by definition it would include the common ancestor of both lineages. Ranoidei have the trigeminal and facial ganglia fused and extant taxa lack free ribs. This group includes all other frogs.
Only the superfamiliesPelobatoidea and Pipoidea are reallocated by the new arrangement. The former are now regarded as representing the ranoidean stem group. Both laival and adult morphology show that pipoids are highly derived rather than primitive frogs, and their trigeminofacial systems show that they are ranoideans rather than discoglossoideans. They presumably are ultimately derived from pelobatoids, but the known taxa are too specialized for direct derivation and there must have been an intermediate group with pipoid tadpoles but without extreme specializations for either fossorial or aquatic life.     

Aluminium accumulation in leaves of 127 species in Melastomataceae,with comments on the order Myrtales

The distribution and systematic significance of aluminium accumulation is surveyed based on semi-quantitative tests of 166 species, representing all tribes and subfamilies of the Melastomataceae as well as a few members of related families within the Myrtales. The character is strongly present in nearly all members of the Memecylaceae and in most primitive taxa of the Melastomataceae, while non-accumulating taxa are widespread in the more derived tribes of the Melastomataceae. The variable distribution of Al accumulation in advanced clades of the latter family is probably associated with the tendency to herbaceousness, although it is unclear whether the more herbaceous representatives have developed more specialized Al-response mechanisms that may exclude high Al levels from the shoot. It is hypothesized that Al accumulation is symplesiomorphic for Melastomataceae and Memecylaceae, and that the feature characterizes the most primitive families in the Myrtales. Indeed, Al accumulation is also characteristic of Crypteroniaceae, Rhynchocalycaceae and Vochysiaceae. Crypteroniaceae and Rhynchocalycaceae probably take a basal position in a sister clade of the Memecylaceae and Melastomataceae, while Al accumulation suggests a basal position for Vochysiaceae in the Myrtaceae clade.     

When Can Clades Be Potentially Resolved with Morphology?

Morphology-based phylogenetic analyses are the only option for reconstructing relationships among extinct lineages, but often find support for conflicting hypotheses of relationships. The resulting lack of phylogenetic resolution is generally explained in terms of data quality and methodological issues, such as character selection. A previous suggestion is that sampling ancestral morphotaxa or sampling multiple taxa descended from a long-lived, unchanging lineage can also yield clades which have no opportunity to share synapomorphies. This lack of character information leads to a lack of ‘intrinsic’ resolution, an issue that cannot be solved with additional morphological data. It is unclear how often we should expect clades to be intrinsically resolvable in realistic circumstances, as intrinsic resolution must increase as taxonomic sampling decreases. Using branching simulations, I quantify intrinsic resolution across several models of morphological differentiation and taxonomic sampling. Intrinsically unresolvable clades are found to be relatively frequent in simulations of both extinct and living taxa under realistic sampling scenarios, implying that intrinsic resolution is an issue for morphology-based analyses of phylogeny. Simulations which vary the rates of sampling and differentiation were tested for their agreement to observed distributions of durations from well-sampled fossil records and also having high intrinsic resolution. This combination only occurs in those datasets when differentiation and sampling rates are both unrealistically high relative to branching and extinction rates. Thus, the poor phylogenetic resolution occasionally observed in morphological phylogenetics may result from a lack of intrinsic resolvability within groups.     

Review of data for a morphological look on Xenacoelomorpha (Bilateria incertae sedis)

Recent investigations by means of high-tech morphology, evo-devo studies and molecular data suggest that the taxon Xenacoelomorpha (Nemertodermatida and Acoela plus Xenoturbella), formerly considered as primitive flatworms (Plathelminthes) or even bivalve Mollusca, represents either a quite plesiomorphic grouping as the earliest bilaterian offshoot or but is a substantially reduced and simplified sidebranch of ambulacralian Deuterostomia. Herein, I provide a compilation and review of the current morphological data and possible interpretations of the various character states. Phenotypic and genotypic data suggest monophyly of Xenacoelomorpha. There is no specific similarity between xenacoelmorphs and deuerostome larvae, and reduction appears improbable in free-living and predatory animals. Accordingly, Xenacoelomorpha are more likely similar to Urbilateria rather than degenerated and simplified coelomate deuterostomes. If so, the ground pattern of Bilateria has been retained only partially in the remaining main bilaterian clades (Nephrozoa) after the deviation of the Xenacoelomorpha, namely the nervous system in the Deuterostomia and the body cavity conditions in the acoelomate Lophotrochozoa (particularly Platyzoa), Gastrotricha and cycloneuralian Ecdysozoa.     

Evolutionary patterns in early tetrapods. II. Differing constraints on available character space among clades

Radiations of large clades often accompany rapid morphological diversification. Evolutionary biologists debate the impact of external restrictions imposed by ecology, and intrinsic constraints imposed by development and genetics, on the rate at which morphological innovations are gained. These issues are particularly interesting for groups such as tetrapods, which evolved novel body plans relative to their piscine ancestors and which also invaded new ecosystems following terrestrialization. Prior studies have addressed these issues by looking at either ranges of morphological variation or rates of character change. Here, we address a related but distinct issue: the numbers of characters that freely vary within a clade. We modify techniques similar to those used by ecologists to infer species richnesses to estimate the number of potentially varying characters given the distributions of changes implied by a model phylogeny. Our results suggest both increasing constraints/restrictions and episodes of 'character release' (i.e. increasing the number of potentially varying characters). In particular, we show that stem lissamphibians had a restricted character space relative to that of stem amniotes, and that stem amniotes both had restrictions on some parts of character space but also invaded new character space that had been unavailable to stem tetrapods.     

Physician assisted suicide: a new look at the arguments

In this paper, I examine the argumens agains physician assisted suicide (PAS). Many of these arguments are consequentialist. Consequentialist arguments rely on empirical claims about the future and thus their strength depends on how likely it is that the predictions will be realized. I discuss these predictions against the backdrop of Oregon's Death with Dignity Act and the practice of PAS in the Netherlands. I then turn to a specific consequentialist argument against PAS - Susan M. Wolfs feminist critique of the practice. Finally, I examine the two most prominent deontological arguments against PAS. Ultimately, I conclude that no anti-PAS argument has merit. Although I do not provide positive arguments for PAS, if none of the arguments against it are strong, we have no reason not to legalize it.     

Clarifications on habitat complexity: A response to technical note by Madin et al.

In a critique of our recent review on measuring habitat complexity in ecology, Madin et al. (2023) advocate the use of fractal dimension in ecology and defend their geometric constraint theory of habitat complexity. We explain the flaws in their arguments and highlight points where they misinterpreted our statements.     

Contesting expertise: anthropologists at the Special Court for Sierra Leone

This article examines how social anthropologists' expertise was employed in the international war crimes trials heard at the Special Court for Sierra Leone. It tracks how the anthropologists challenged the prosecution experts by raising concerns about their methodology and advancing a fundamental critique of abstract legal categories. The discussion between the experts centred on two contested issues: the character of the armed groups and the phenomenon of forced marriages during the civil war in Sierra Leone. The analysis of the experts' testimonies shows that the anthropologists were engaged in an epistemological contest with the prosecution experts. The article aims at understanding why the anthropologists' arguments had less resonance with the judges than the reports submitted by the prosecution experts. Beyond the courtroom, it also speaks to the general debate about expertise and ways to study it.     

Minimal effects of latitude on present-day speciation rates in New World birds

The tropics contain far greater numbers of species than temperate regions, suggesting that rates of species formation might differ systematically between tropical and non-tropical areas. We tested this hypothesis by reconstructing the history of speciation in New World (NW) land birds using BAMM, a Bayesian framework for modelling complex evolutionary dynamics on phylogenetic trees. We estimated marginal distributions of present-day speciation rates for each of 2571 species of birds. The present-day rate of speciation varies approximately 30-fold across NW birds, but there is no difference in the rate distributions for tropical and temperate taxa. Using macroevolutionary cohort analysis, we demonstrate that clades with high tropical membership do not produce species more rapidly than temperate clades. For nearly any value of present-day speciation rate, there are far more species in the tropics than the temperate zone. Any effects of latitude on speciation rate are marginal in comparison to the dramatic variation in rates among clades.