Ancestor-descendant Relationships Research Articles

The Effect of Nonreversibility on Inferring Rooted Phylogenies.

Most phylogenetic models assume that the evolutionary process is stationary and reversible. In addition to being biologically improbable, these assumptions also impair inference by generating models under which the likelihood does not depend on the position of the root. Consequently, the root of the tree cannot be inferred as part of the analysis. Yet identifying the root position is a key component of phylogenetic inference because it provides a point of reference for polarizing ancestor–descendant relationships and therefore interpreting the tree. In this paper, we investigate the effect of relaxing the unrealistic reversibility assumption and allowing the position of the root to be another unknown. We propose two hierarchical models that are centered on a reversible model but perturbed to allow nonreversibility. The models differ in the degree of structure imposed on the perturbations. The analysis is performed in the Bayesian framework using Markov chain Monte Carlo methods for which software is provided. We illustrate the performance of the two nonreversible models in analyses of simulated data using two types of topological priors. We then apply the models to a real biological data set, the radiation of polyploid yeasts, for which there is robust biological opinion about the root position. Finally, we apply the models to a second biological alignment for which the rooted tree is controversial: the ribosomal tree of life. We compare the two nonreversible models and conclude that both are useful in inferring the position of the root from real biological data.

New crinoids from the Baltic region (Estonia): fossil tip‐dating phylogenetics constrains the origin and Ordovician–Silurian diversification of the Flexibilia (Echinodermata)

AbstractThis study documents previously unknown taxonomic and morphological diversity among early Palaeozoic crinoids. Based on highly complete, well preserved crown material, we describe two new genera from the Ordovician and Silurian of the Baltic region (Estonia) that provide insight into two major features of the geological history of crinoids: the early evolution of the flexible clade during the Great Ordovician Biodiversification Event (GOBE), and their diversification history surrounding the end‐Ordovician mass extinction. The unexpected occurrence of a highly derived sagenocrinid, Tintinnabulicrinus estoniensis gen. et. sp. nov., from Upper Ordovician (lower Katian) rocks of the Baltic palaeocontinent provides high‐resolution temporal, taxonomic and palaeobiogeographical constraints on the origin and early evolution of the Flexibilia. The Silurian (lower Rhuddanian, Llandovery) Paerticrinus arvosus gen. et sp. nov. is the oldest known Silurian crinoid from Baltica and thus provides the earliest Baltic record of crinoids following the aftermath of the end‐Ordovician mass extinction. A Bayesian ‘fossil tip‐dating’ analysis implementing the fossilized birth–death process and a relaxed morphological clock model suggests that flexibles evolved c. 3 million years prior to their oldest fossil record, potentially involving an ancestor–descendant relationship (via ‘budding’ cladogenesis or anagenesis) with the paraphyletic cladid Cupulocrinus. The sagenocrinid subclade rapidly diverged from ‘taxocrinid’ grade crinoids during the final stages of the GOBE, culminating in maximal diversity among Ordovician crinoid faunas on a global scale. Remarkably, diversification patterns indicate little taxonomic turnover among flexibles across the Late Ordovician mass extinction. However, the elimination of closely related clades may have helped pave the way for their subsequent Silurian diversification and increased ecological role in post‐Ordovician Palaeozoic marine communities. This study highlights the significance of studies reporting faunas from undersampled palaeogeographical regions for clade‐based phylogenetic studies and improving estimates of global biodiversity through geological time.

A simple parsimony-based approach to assess ancestor-descendant relationships

One of the main goals of systematics is to reconstruct the tree of life. Half a century ago, the breakthrough of cladistics was a major step towards this objective because it allowed us to assess relatedness patterns among species, an abstract kind of relationship. Unfortunately, the philosophy of cladism forbade to go further and to seek more realistic relationships, like the ancestor-descendant relationship, which is the expected fundamental kind of relationship of the tree of life according to Darwinian evolution. Here, I describe a simple parsimony-based procedure which can be used to transform a classical cladogram into a genuine phylogenetic tree, i.e. a caulogram. It consists in deleting as many unobserved and unnamed nodes as possible and replacing them with observed and named species. A new Bayesian non-stochastic weighting scheme is used to assess character reliability for both this procedure and classical cladogram construction. I illustrate the whole process by assessing the relationships between the species of the moss genus Didymodon sensu lato (Pottiaceae) and discuss the resulting caulogram by confronting it with the previous methodology from the evolutionary literature. I finally argue that strictly adhering to cladist epistemology is untenable and that we must seek new formal methods to find ancestral species as well as ancestral higher taxa.

Specimen-level phylogenetics in paleontology using the Fossilized Birth-Death model with sampled ancestors.

Bayesian phylogenetic methods integrating simultaneously morphological and stratigraphic information have been applied increasingly among paleontologists. Most of these studies have used Bayesian methods as an alternative to the widely-used parsimony analysis, to infer macroevolutionary patterns and relationships among species-level or higher taxa. Among recently introduced Bayesian methodologies, the Fossilized Birth-Death (FBD) model allows incorporation of hypotheses on ancestor-descendant relationships in phylogenetic analyses including fossil taxa. Here, the FBD model is used to infer the relationships among an ingroup formed exclusively by fossil individuals, i.e., dipnoan tooth plates from four localities in the Ain el Guettar Formation of Tunisia. Previous analyses of this sample compared the results of phylogenetic analysis using parsimony with stratigraphic methods, inferred a high diversity (five or more genera) in the Ain el Guettar Formation, and interpreted it as an artifact inflated by depositional factors. In the analysis performed here, the uncertainty on the chronostratigraphic relationships among the specimens was included among the prior settings. The results of the analysis confirm the referral of most of the specimens to the taxa Asiatoceratodus, Equinoxiodus, Lavocatodus and Neoceratodus, but reject those to Ceratodus and Ferganoceratodus. The resulting phylogeny constrained the evolution of the Tunisian sample exclusively in the Early Cretaceous, contrasting with the previous scenario inferred by the stratigraphically-calibrated topology resulting from parsimony analysis. The phylogenetic framework also suggests that (1) the sampled localities are laterally equivalent, (2) but three localities are restricted to the youngest part of the section; both results are in agreement with previous stratigraphic analyses of these localities. The FBD model of specimen-level units provides a novel tool for phylogenetic inference among fossils but also for independent tests of stratigraphic scenarios.

Dental topographic analysis of paromomyid (Plesiadapiformes, Primates) cheek teeth: more than 15 million years of changing surfaces and shifting ecologies

Plesiadapiforms, appearing near the Cretaceous-Paleogene boundary, represent the first primate radiation and show a diverse array of tooth morphologies. Dental topographic metrics provide quantitative data on occlusal surface shape. We used three metrics, Dirichlet Normal Energy, Relief Index, and 3D Orientation Patch Count Rotated, to assess changes in the morphology of lower fourth premolars and lower second molars in a taxonomically broad sample of one family of plesiadapiforms, Paromomyidae, stretching more than 15 million years. Our results indicate that paromomyids occupied a more diverse range of dietary categories than suspected. Whereas all paromomyids were likely omnivores, some species show higher levels of insectivory, while other taxa are inferred to have been mixed-feeding omnivores with high levels of fruit intake. The results also show that the more primitive members of the different paromomyid lineages were more insectivorous than the derived and more recent members of those lineages. Relief Index values also show taxonomic signals that are consistent with ancestor-descendant relationships hypothesised for species of Phenacolemur. These results suggest that dental topographic metrics are informative to the study of paromomyids for both dietary categorisation and for the distinction of species at a fine taxonomic level.

Categorizing ideas about systematics: alternative trees of trees, and related representations

This study is an attempt to expand a previous survey by Fisler and Lecointre (FL) for systematizing ideas on the use of the tree metaphor in classification, as expressed by various historically important figures in their writings. FL used a cladistic approach to analyze their data, as employed in biological classification. We supplement this analysis here using several methods of multivariate data exploration, producing a UPGMA dendrogram, a minimum spanning tree, a neighbor joining additive tree, a plexus graph, a phylogenetic network, and two multidimensional scaling ordinations of the same data used by FL. We confirm the validity of many of FL’s smaller clusters of writings, and revealed a new 3-group categorization undetected by the previous study. These three groups largely correspond to Classifiers, who did not consider evolution for historical reasons or on purpose, Non-analytical evolutionists, who recognized evolution but with a more or less naive attitude towards the temporal change of life, and Modelers, with more explicit views on evolutionary processes, often applying objective mathematical tools for exploring the past and present of organismal diversity. Some scientists were difficult to assign to any group unambiguously, including J. W. von Goethe, who takes a unique position in the history of biology, and, to a lesser extent, E. Mayr and G. G. Simpson, the leaders of the gradist school of systematics. We argue that cladistic methods are insufficient by themselves, notably in situations where there are no obvious ancestor–descendant relationships underlying the development of the objects being analyzed.

Multiple origins of gigantism in stem baleen whales.

Living baleen whales (Mysticeti) include the world's largest animals to have ever lived-blue whales (Balaenoptera musculus) can reach more than 30m. However, the gigantism in baleen whales remains little explored. Here, we compiled all published stem mysticetes from the Eocene and Oligocene and then mapped the estimated body size onto different phylogenies that suggest distinct evolutionary histories of baleen whales. By assembling all known stem baleen whales, we present three novel findings in early mysticete evolution. Results show that, regardless of different phylogenetic scenarios, large body size (more than 5-m long) evolved multiple times independently in their early evolutionary history. For example, the earliest known aetiocetid (Fucaia buelli, 33-31Ma) was small in size, about 2m, and a later aetiocetid (Morawanocetus-like animal, 26-23Ma) can reach 8-m long-almost four times the size of Fucaia buelli-suggesting an independent gigantism in the aetiocetid lineage. In addition, our reconstruction of ancestral state demonstrates that the baleen whales originated from small body size (less than 5m) rather than large body size as previously acknowledged. Moreover, reconstructing the evolution of body size in stem baleen whales suggests that the initial pulse of mysticete gigantism started at least back to the Paleogene and in turn should help to understand the origin, pattern, and process of the extreme gigantism in the crown baleen whales. This study illustrates that Cope's rule is insufficient to explain the evolution of body size in a group that comprises the largest animals in the history of life, although currently the lack of exact ancestor-descendant relationships remains to fully reveal the evolutionary history of body size.

Study of XML Indexing Structure Based on XISS

The study is based on XISS(XML Indexing and Storage System) of Dietz’s Numbering Schema to determine the ancestor-descendant relationship. According to the results of research, this paper proposes an improved method of node encoding, realizes its indexing structure, and discusses its query path. Finally, the paper analyzes the property of this improved method.

BEVA

Query autocompletion has become a standard feature in many search applications, especially for search engines. A recent trend is to support the error-tolerant autocompletion , which increases the usability significantly by matching prefixes of database strings and allowing a small number of errors. In this article, we systematically study the query processing problem for error-tolerant autocompletion with a given edit distance threshold. We propose a general framework that encompasses existing methods and characterizes different classes of algorithms and the minimum amount of information they need to maintain under different constraints. We then propose a novel evaluation strategy that achieves the minimum active node size by eliminating ancestor-descendant relationships among active nodes entirely. In addition, we characterize the essence of edit distance computation by a novel data structure named edit vector automaton (EVA). It enables us to compute new active nodes and their associated states efficiently by table lookups. In order to support large distance thresholds, we devise a partitioning scheme to reduce the size and construction cost of the automaton, which results in the universal partitioned EVA (UPEVA) to handle arbitrarily large thresholds. Our extensive evaluation demonstrates that our proposed method outperforms existing approaches in both space and time efficiencies.

How to Identify and Interpret Evolutionary Tree Diagrams

Evolutionary trees are key tools for modern biology and are commonly portrayed in textbooks to promote learning about biological evolution. However, many people have difficulty in understanding what evolutionary trees are meant to portray. In fact, some ideas that current professional biologists depict with evolutionary trees are neither clearly defined nor conveyed to students. To help biology teachers and students learn how to more deeply interpret, understand and gain knowledge from diagrams that represent ancestor–descendant relationships and evolutionary lineages, we describe the different rooted and unrooted evolutionary tree visualisations and explain how they are best read. Examples from a study of tree-shaped diagrams in the journal Science are used to illustrate how to distinguish evolutionary trees from other tree-shaped representations that are easily misunderstood as visualising evolutionary relationships. We end by making recommendations for how our findings may be implemented in teaching practice in this important area of biology education.

Dating of Cambrian-Ordovician boundary strata in northernmost Vietnam and methodological aspects of evolutionary biostratigraphic inference

Unrepeatability of evolution and the correspondence of the fossil record to ancestor-descendant successions of species are the unavoidable, although usually hidden, assumptions in any reliable age determination based on fossils. We expose these assumptions while dating early Paleozoic carbonate rock deposits in the Lung Cu section at the Vietnamese/Chinese border. The best-preserved and most abundant fossils in this section are shumardiid trilobites. The succession of shumardiid species, based on data from elsewhere, provides an evolutionary reference standard. The shumardiid record is not sufficiently complete to verify hypotheses of ancestor-descendant relationships but enables estimation of the "degree of evolutionary advancement" of the Vietnamese species. This suggests an age close to the Cambrian/Ordovician boundary. Although considered non-scientific by cladists, such inferences are testable. Support for a late Furongian or early Tremadocian age is provided by the occurrence of Cordylodus conodonts in strata above the trilobite-bearing bed. The conodont evolution has a good fossil record interpreted in population terms in the Baltic region and Australia, including the lineage represented in Vietnam. Age determination based on such evolutionary reasoning is reliable but of a relatively low resolution, because the rate of morphological evolution is generally low. Generally, more precise dating is offered by distribution of fossils controlled by ecological factors, which are repeatable and mostly diachronous over large geographic distances, but they may have happened relatively rapidly. The appearance of the Iapetognathus-Chosonodina-bearing conodont assemblage in the Lung Cu area, as suggested by its occurrences elsewhere, was probably due to abrupt faunal migration into the region.

Mining rooted ordered trees under subtree homeomorphism

Mining frequent tree patterns has many applications in different areas such as XML data, bioinformatics and World Wide Web. The crucial step in frequent pattern mining is frequency counting, which involves a matching operator to find occurrences (instances) of a tree pattern in a given collection of trees. A widely used matching operator for tree-structured data is subtree homeomorphism, where an edge in the tree pattern is mapped onto an ancestor-descendant relationship in the given tree. Tree patterns that are frequent under subtree homeomorphism are usually called embedded patterns. In this paper, we present an efficient algorithm for subtree homeomorphism with application to frequent pattern mining. We propose a compact data-structure, called occ, which stores only information about the rightmost paths of occurrences and hence can encode and represent several occurrences of a tree pattern. We then define efficient join operations on the occ data-structure, which help us count occurrences of tree patterns according to occurrences of their proper subtrees. Based on the proposed subtree homeomorphism method, we develop an effective pattern mining algorithm, called TPMiner. We evaluate the efficiency of TPMiner on several real-world and synthetic datasets. Our extensive experiments confirm that TPMiner always outperforms well-known existing algorithms, and in several cases the improvement with respect to existing algorithms is significant.

Fraction and Prefix Encoding Scheme of Supporting Updating Data Efficiently

At present, more and more data are expressed in the form of XML format, and how to manage these data effi- ciently becomes an important issue. In order to update and query XML data efficiently, we proposed a new encoding scheme called MPES (modify prefix encoding scheme). MPES makes full good use of the advantages of fraction encod- ing and prefix encoding and it supports updating data efficiently. Furthermore, MPES also supports the representation of sibling relationship, parent-children relationship and ancestor-descendant relationship between any two nodes. The exper- imental results show that, compared with fraction encoding scheme, MPES improves the updating efficiency of XML da- ta. As compared with prefix encoding scheme, MPES improved the querying efficiency of XML data.

The extended Price equation quantifies species selection on mammalian body size across the Palaeocene/Eocene Thermal Maximum.

Species selection, covariation of species' traits with their net diversification rates, is an important component of macroevolution. Most studies have relied on indirect evidence for its operation and have not quantified its strength relative to other macroevolutionary forces. We use an extension of the Price equation to quantify the mechanisms of body size macroevolution in mammals from the latest Palaeocene and earliest Eocene of the Bighorn and Clarks Fork Basins of Wyoming. Dwarfing of mammalian taxa across the Palaeocene/Eocene Thermal Maximum (PETM), an intense, brief warming event that occurred at approximately 56 Ma, has been suggested to reflect anagenetic change and the immigration of small bodied-mammals, but might also be attributable to species selection. Using previously reconstructed ancestor-descendant relationships, we partitioned change in mean mammalian body size into three distinct mechanisms: species selection operating on resident mammals, anagenetic change within resident mammalian lineages and change due to immigrants. The remarkable decrease in mean body size across the warming event occurred through anagenetic change and immigration. Species selection also was strong across the PETM but, intriguingly, favoured larger-bodied species, implying some unknown mechanism(s) by which warming events affect macroevolution.

Testing modern human out-of-Africa dispersal models and implications for modern human origins

The modern human expansion process out of Africa has important implications for understanding the genetic and phenotypic structure of extant populations. While intensely debated, the primary hypotheses focus on either a single dispersal or multiple dispersals out of the continent. Here, we use the human fossil record from Africa and the Levant, as well as an exceptionally large dataset of Holocene human crania sampled from Asia, to model ancestor–descendant relationships along hypothetical dispersal routes. We test the spatial and temporal predictions of competing out-of-Africa models by assessing the correlation of geographical distances between populations and measures of population differentiation derived from quantitative cranial phenotype data. Our results support a model in which extant Australo-Melanesians are descendants of an initial dispersal out of Africa by early anatomically modern humans, while all other populations are descendants of a later migration wave. Our results have implications for understanding the complexity of modern human origins and diversity.

Computing discounted multidimensional hierarchical aggregates using modified Misra Gries algorithm

Finding the “Top k” list or heavy hitters is an important function in many computing applications, including database joins, data warehousing (e.g., OLAP), web caching and hits, network usage monitoring, and detecting DDoS attacks. While most applications work on traditional “flat” data, many domains contain data that has attributes which can take values from different hierarchies e.g., time and geographic location, source and destination IP addresses, etc. In addition, hierarchical heavy hitters generated from hierarchical attributes offer insightful and a generalized view of the data. When data arrives in a stream, infrequent data elements need to be deleted due to space constraints. However, unlike traditional heavy hitters which do not consider deleted elements, in a hierarchical heavy hitter some of these deleted elements could form a heavy hitter at a higher level of the hierarchy. Furthermore, unlike traditional heavy hitters, hierarchical heavy hitters have ancestor–descendant relationship which requires the count of descendant heavy hitters to be discounted at the higher levels of the hierarchy. This is particularly challenging in a streaming environment because all the incoming data items cannot be stored or revisited. This problem is generally addressed by accepting an error constraint ϵ on the precision of the count of hierarchical heavy hitters, since accurate count cannot be guaranteed under the constrained memory requirement posed by the streaming environment. In this work, we propose a new streaming ϵ-approximation algorithm (HHH-MG) for computing Hierarchical Heavy Hitters based on a modified Misra Gries heavy hitter algorithm. The proposed algorithm guarantees ϵ-approximation precision with improved worst-case time and space bounds compared to previous algorithms. It requires overall O(ηϵ) space, and O(η) updates per element of the data, where η is a small constant. We provide theoretical proofs for the space and time requirements. We have also experimentally compared the proposed algorithm with benchmark techniques. Experimental results demonstrate that the proposed algorithm requires fewer updates per element of data, and on average requires less memory. For the experimental validation, we have used both synthetic data derived from an open source generator, and real benchmark datasets from an international Internet Service Provider.

Oral fairy tale or literary fake? Investigating the origins ofLittle Red Riding Hoodusing phylogenetic network analysis

The evolution of fairy tales often involves complex interactions between oral and literary traditions, which can be difficult to tease apart when investigating their origins. Here, we show how computer-assisted stemmatology can be productively applied to this problem, focusing on a long-standing controversy in fairy tale scholarship: did Little Red Riding Hood originate as an oral tale that was adapted by Perrault and the Brothers Grimm, or is the oral tradition in fact derived from literary texts? We address this question by analysing a sample of twenty-four literal and oral versions of the fairy tale Little Red Riding Hood using several methods of phylogenetic analysis, including maximum parsimony and two network-based approaches (NeighbourNet and TRex). While the results of these analyses are more compatible with the oral origins hypothesis than the alternative literary origins hypothesis, their interpretation is problematized by the fact that none of them explicitly model lineal (i.e. ancestor-descendent) relationships among taxa. We therefore present a new likelihood-based method, PhyloDAG, which was specifically developed to model lineal as well as collateral and reticulate relationships. A comparison of different structures derived from PhyloDAG provided a much clearer result than the maximum parsimony, NeighbourNet or TRex analyses, and strongly favoured the hypothesis that literary versions of Little Red Riding Hood were originally based on oral folktales, rather than vice versa.

Ancestor-descendant relationships in evolution: origin of the extant pygmy right whale, Caperea marginata.

Ancestor-descendant relationships (ADRs), involving descent with modification, are the fundamental concept in evolution, but are usually difficult to recognize. We examined the cladistic relationship between the only reported fossil pygmy right whale, †Miocaperea pulchra, and its sole living relative, the enigmatic pygmy right whale Caperea marginata, the latter represented by both adult and juvenile specimens. †Miocaperea is phylogenetically bracketed between juvenile and adult Caperea marginata in morphologically based analyses, thus suggesting a possible ADR-the first so far identified within baleen whales (Cetacea: Mysticeti). The †Miocaperea-Caperea lineage may show long-term morphological stasis and, in turn, punctuated equilibrium.

Two new species of Prolagus (Lagomorpha, Mammalia) from the Late Miocene of Hungary: taxonomy, biochronology, and palaeobiogeography

The present study describes two new species, Prolagus pannonicus sp. nov. and P. latiuncinatus sp. nov., from the Late Miocene Hungarian localities Sumeg (MN10/11) and Polgardi 2 (MN13). These species are closely related, probably by a direct ancestor–descendant relationship. They share characters common to Late Miocene–Pliocene eastern European species (e.g., the retention of the entoconid enamel in p3 contrarily to coeval western European ones), attesting to an eastern European group of Prolagus that evolved independently from western European species at least since MN10/11. Nevertheless, the two Hungarian species of Prolagus here described follow particular evolutionary trends: contrarily to other European Late Miocene species, their p3 does not undergo a substantial size increase after MN12, whereas the crochet size enlarges noticeably. Special emphasis is given to the comparison of P. pannonicus sp. nov. and P. latiuncinatus sp. nov. with the Gargano insular endemic Prolagus species. Their common morphological traits are related to convergence due to endemism. Prolagus pannonicus sp. nov. and P. latiuncinatus sp. nov. probably were continental isolated species.

Evolutionary trends in Triceratops from the Hell Creek Formation, Montana.

The placement of over 50 skulls of the well-known horned dinosaur Triceratops within a stratigraphic framework for the Upper Cretaceous Hell Creek Formation (HCF) of Montana reveals the evolutionary transformation of this genus. Specimens referable to the two recognized morphospecies of Triceratops, T. horridus and T. prorsus, are stratigraphically separated within the HCF with the T. prorsus morphology recovered in the upper third of the formation and T. horridus found lower in the formation. Hypotheses that these morphospecies represent sexual or ontogenetic variation within a single species are thus untenable. Stratigraphic placement of specimens appears to reveal ancestor-descendant relationships. Transitional morphologies are found in the middle unit of the formation, a finding that is consistent with the evolution of Triceratops being characterized by anagenesis, the transformation of a lineage over time. Variation among specimens from this critical stratigraphic zone may indicate a branching event in the Triceratops lineage. Purely cladogenetic interpretations of the HCF dataset imply greater diversity within the formation. These findings underscore the critical role of stratigraphic data in deciphering evolutionary patterns in the Dinosauria.