Academic literature on the topic 'Ancestoral state reconstruction'

Anthropological Reconstruction Laboratory of the Center for Physical Anthropology, Institute of Ethnology and Anthropology RAS. The article relates the current state of the M.M. Gerasimov Laboratory of Anthropological Reconstruction of the Center for Physical Anthropology, Institute of Ethnology and Anthropology, Russian Academy of Sciences. Emphasizing the role of the founder of the method of face reconstruction from the skull, the author discusses the latest improvements to this method. The data bank on the thickness of the facial integument in representatives of various ethnic groups, and the accumulated experience with regard to the relationships between facial features and the underlying structures of the skull, made it possible to create a program of craniofacial correspondence ‘The Algorithm of Appearance’, which significantly improves the process of reconstructing in vivo appearance based on the skull. The visual reconstruction of the appearance is supplemented by an anthropological description of the lifetime appearance, in terms of the ‘verbal portrait’ used in forensic science. A description of a unique collection of more than 300 sculptural and graphic portraits made on the basis of the skulls of ancient people and historical figures is given. Based on the examples of specific projects, the possibilities of anthropological reconstruction for solving applied and theoretical problems of science are shown. The reconstruction of the appearance of soldiers killed in the Second World War is the key patriotic direction of the Laboratory s work. Based on the results of these reconstructions, several fi were identifi Th Laboratory is currently at work on reconstructing the lifetime appearance of A.V. Suvorov on the basis of a death mask.

Pseudoextinction analyses, which simulate extinction in extant taxa, use molecular phylogenetics to assess the accuracy of morphological phylogenetics. Previous pseudoextinction analyses have shown a failure of morphological phylogenetics to place some individual placental orders in the correct superordinal clade. Recent work suggests that the inclusion of hypothetical ancestors of extant placental clades, estimated by ancestral state reconstructions of morphological characters, may increase the accuracy of morphological phylogenetic analyses. However, these studies reconstructed direct hypothetical ancestors for each extant taxon based on a well-corroborated molecular phylogeny, which is not possible for extinct taxa that lack molecular data. It remains to be determined if pseudoextinct taxa, and by proxy extinct taxa, can be accurately placed when their immediate hypothetical ancestors are unknown. To investigate this, we employed molecular scaffolds with the largest available morphological data set for placental mammals. Each placental order was sequentially treated as pseudoextinct by exempting it from the molecular scaffold and recoding soft morphological characters as missing for all its constituent species. For each pseudoextinct data set, we omitted the pseudoextinct taxon and performed a parsimony ancestral state reconstruction to obtain hypothetical predicted ancestors. Each pseudoextinct order was then evaluated in seven parsimony analyses that employed combinations of fossil taxa, hypothetical predicted ancestors, and a molecular scaffold. In treatments that included fossils, hypothetical predicted ancestors, and a molecular scaffold, only 8 of 19 pseudoextinct placental orders (42%) retained the same interordinal placement as on the molecular scaffold. In treatments that included hypothetical predicted ancestors but not fossils or a scaffold, only four placental orders (21%) were recovered in positions that are congruent with the scaffold. These results indicate that hypothetical predicted ancestors do not increase the accuracy of pseudoextinct taxon placement when the immediate hypothetical ancestor of the taxon is unknown. Hypothetical predicted ancestors are not a panacea for morphological phylogenetics.

AbstractDuring the past century, numerous theoretical articles explored the evolution of seasonal migration in birds; many of these focused on environmental or social conditions that may have led to the origin of migration. More recent work has focused not on the origin of migration, but on changes in migratory behavior that have occurred in modern species and their immediate ancestors. We used a novel approach, a multistate ancestral state reconstruction of migration, to examine patterns of migratory evolution in the New World orioles (Icterus spp.). Both the multistate and binary reconstructions indicated repeated gains in migration. However, the multistate method revealed details of how migration may be gained that the standard binary-state reconstructions would not have shown. Our maximum-likelihood reconstruction, using branch lengths based on a molecular phylogeny, suggested multiple instances of rapid gain of migration. Furthermore, we found that every migratory species' migration type differed from that of its closest relatives. Surprisingly, no partially migratory species was closely related to a fully migratory species. These novel patterns involving gain of migration demonstrate the utility of multistate ancestral reconstruction for examining changes in migratory behavior in closely related birds.Reconstrucción de Estados Ancestrales de la Migración: Análisis con Múltiples Estados de Carácter Revelan Cambios Rápidos en los Orioles del Nuevo Mundo (Icterus spp.)

Diapause is a physiological arrest of development ahead of adverse environmental conditions and is a critical phase of the life cycle of many insects. In bees, diapause has been reported in species from all seven taxonomic families. However, they exhibit a variety of diapause strategies. These different strategies are of particular interest since shifts in the phase of the insect life cycle in which diapause occurs have been hypothesized to promote the evolution of sociality. Here we provide a comprehensive evaluation of this hypothesis with phylogenetic analysis and ancestral state reconstruction (ASR) of the ecological and evolutionary factors associated with diapause phase. We find that social lifestyle, latitude and voltinism are significant predictors of the life stage in which diapause occurs. ASR revealed that the most recent common ancestor of all bees likely exhibited developmental diapause and shifts to adult, reproductive, or no diapause have occurred in the ancestors of lineages in which social behaviour has evolved. These results provide fresh insight regarding the role of diapause as a prerequisite for the evolution of sociality in bees.

Reconstructing the behavioral shifts that drove hominin evolution requires knowledge of the timing, magnitude, and direction of anatomical changes over the past ∼6–7 million years. These reconstructions depend on assumptions regarding the morphotype of the Homo–Pan last common ancestor (LCA). However, there is little consensus for the LCA, with proposed models ranging from African ape to orangutan or generalized Miocene ape-like. The ancestral state of the shoulder is of particular interest because it is functionally associated with important behavioral shifts in hominins, such as reduced arboreality, high-speed throwing, and tool use. However, previous morphometric analyses of both living and fossil taxa have yielded contradictory results. Here, we generated a 3D morphospace of ape and human scapular shape to plot evolutionary trajectories, predict ancestral morphologies, and directly test alternative evolutionary hypotheses using the hominin fossil evidence. We show that the most parsimonious model for the evolution of hominin shoulder shape starts with an African ape-like ancestral state. We propose that the shoulder evolved gradually along a single morphocline, achieving modern human-like configuration and function within the genus Homo. These data are consistent with a slow, progressive loss of arboreality and increased tool use throughout human evolution.

Due to the controversy surrounding incipient avian parental care, ancestral parental care systems were reconstructed in a phylogeny including major extant amniote lineages. Using two different resolutions for the basal avian branches, transitions between the states no care, female care, biparental care and male care were inferred for the most basal branches of the tree. Uniparental female care was inferred for the lineage to birds and crocodiles. Using a phylogeny where ratites and tinamous branch off early and an ordered character–state assumption, a transition to biparental care was inferred for the ancestor of birds. This ancestor could be any organism along the lineage leading from the crocodile–bird split up to modern birds, not necessarily the original bird. We discuss the support for alternative avian phylogenies and the homology in parental care between crocodiles and birds. We suggest that the phylogenetic pattern should be used as a starting point for a more detailed analysis of parental care systems in birds and their relatives.

A comparison of sequenced Agaricomycotina genomes suggests that efficient degradation of wood lignin was associated with the appearance of secreted peroxidases with a solvent-exposed catalytic tryptophan. This hypothesis is experimentally demonstrated here by resurrecting ancestral fungal peroxidases, after sequence reconstruction from genomes of extant white-rot Polyporales, and evaluating their oxidative attack on the lignin polymer by state-of-the-art analytical techniques. Rapid stopped-flow estimation of the transient-state constants for the 2 successive one-electron transfers from lignin to the peroxide-activated enzyme (k2app and k3app) showed a progressive increase during peroxidase evolution (up to 50-fold higher values for the rate-limiting k3app). The above agreed with 2-dimensional NMR analyses during steady-state treatments of hardwood lignin, showing that its degradation (estimated from the normalized aromatic signals of lignin units compared with a control) and syringyl-to-guaiacyl ratio increased with the enzyme evolutionary distance from the first peroxidase ancestor. More interestingly, the stopped-flow estimations of electron transfer rates also showed how the most recent peroxidase ancestors that already incorporated the exposed tryptophan into their molecular structure (as well as the extant lignin peroxidase) were comparatively more efficient at oxidizing hardwood (angiosperm) lignin, while the most ancestral “tryptophanless” enzymes were more efficient at abstracting electrons from softwood (conifer) lignin. A time calibration of the ancestry of Polyporales peroxidases localized the appearance of the first peroxidase with a solvent-exposed catalytic tryptophan to 194 ± 70 Mya, coincident with the diversification of angiosperm plants characterized by the appearance of dimethoxylated syringyl lignin units.

AbstractThe class Eurotiomycetes (Ascomycota, Pezizomycotina) comprises important fungi used for medical, agricultural, industrial and scientific purposes. Eurotiomycetes is a morphologically and ecologically diverse monophyletic group. Within the Eurotiomycetes, different ascoma morphologies are found including cleistothecia and perithecia but also apothecia or stromatic forms. Mazaediate representatives (with a distinct structure in which loose masses of ascospores accumulate to be passively disseminated) have evolved independently several times. Here we describe a new mazaediate species belonging to the Eurotiomycetes. The multigene phylogeny produced (7 gene regions: nuLSU, nuSSU, 5.8S nuITS, mtSSU, RPB1, RPB2 and MCM7) placed the new species in a lineage sister to Eurotiomycetidae. Based on the evolutionary relationships and morphology, a new subclass, a new order, family and genus are described to place the new species: Cryptocalicium blascoi. This calicioid species occurs on the inner side of loose bark strips of Cupressaceae (Cupressus, Juniperus). Morphologically, C. blascoi is characterized by having minute apothecioid stalked ascomata producing mazaedia, clavate bitunicate asci with hemiamyloid reaction, presence of hamathecium and an apothecial external surface with dark violet granules that becomes turquoise green in KOH. The ancestral state reconstruction analyses support a common ancestor with open ascomata for all deep nodes in Eurotiomycetes and the evolution of closed ascomata (cleistothecioid in Eurotiomycetidae and perithecioid in Chaetothyriomycetidae) from apothecioid ancestors. The appropriateness of the description of a new subclass for this fungus is also discussed.

The building at Toumba, Lefkandi, stands unique in its time and place. The remains of this monument are significant in terms of size and elaboration, and also on account of the way it has been reconstructed and interpreted as the ancestor of the Greek peripteral temple. The primary concern of this article is the structural evaluation of the architectural remains. In part due to the scant nature of the archaeological evidence behind the widely accepted reconstruction, the latter can be seen to have several structural shortcomings. In reassessing the structure several factors are considered, including the state of technology at the time of construction, the characteristics of the building materials employed, and the way they respond to the strains of load and the forces of nature. The process of reconciling such factors with the documented remnants of the building directs us towards a different reconstruction. It thus emerges that the building at Toumba is an implausible ancestor of Greek peripteroi, and an alternative solution without the iconic pre-peristasis is proposed here.

Pseudomonas syringae is a common foliar plant pathogenic bacterium that causes diseases on many crop plants. We hypothesized that todayâ s highly virulent P. syringae crop pathogens with narrow host range might have evolved after the advent of agriculture from ancestral P. syringae strains with wide host range that were adapted to mixed plant communities. The model tomato and Arabidopsis pathogen P. syringae pv. tomato (Pto) DC3000 and its close relatives isolated from crop plants were thus selected to unravel basic principles of host range evolution by applying molecular evolutionary analysis and comparative genomics approaches. Phylogenetic analysis was combined with host range tests to reconstruct the host range of the most recent common ancestor of all analyzed strains isolated from crop plants. Even though reconstruction of host range of the most recent common ancestor of all analyzed strains was not conclusive, support for this hypothesis was found in some sub-groups of strains. The focus of my studies then turned to Pto T1, which was found to represent the most common P. syringae lineage causing bacterial speck disease on tomato world-wide. Five genomes were sequenced and compared to each other. Identical genotypes were found in North America and Europe suggesting frequent pathogen movement between these continents. Moreover, the type III-secreted effector gene hopM1 was found to be under strong selection for loss of function and non-synonymous mutations in the fliC gene allowed to identify a region that triggers plant immunity. Finally, Pto T1 was compared to closely related bacteria isolated from snow pack and surface water in the French Alps. Recombination between alpine strains and crop strains was inferred and virulence gene repertoires of alpine strains and crop strains were found to overlap. Alpine strains cause disease on tomato and have relatively wider host ranges than Pto T1. The conclusion from these studies is that Pto T1 and other crop pathogens may have evolved from ancestors similar to the characterized environmental strains isolated in the French Alps by adapting their effector repertoire to individual crops becoming more virulent on these crops but losing virulence on other plants.
Ph. D.

Microorganisms play crucial roles in aquatic environments in determining ecosystemstability and driving the turnover of elements essential to life. Understanding thedistribution and evolution of aquatic microorganisms will help us predict how aquaticecosystems will respond to Global Change, and such understanding can be gained bystudying these processes of the past. In this project, we investigate the evolutionaryrelationship between brackish water bacteria from the Baltic Sea and Caspian Seawith freshwater and marine bacteria, with the goal of understanding how brackishwater bacteria have evolved. 11,276 bacterial metagenome-assembled genomes(MAGs) from seven metagenomic datasets were used to conduct a comparativeanalysis of freshwater, brackish and marine bacteria. When clustering the genomes bypairwise average nucleotide identity (ANI) at the approximate species level (96.5%ANI), the Baltic Sea genomes were more likely to form clusters with the Caspian Seagenomes than with Swedish lakes genomes, even though geographic distancesbetween Swedish lakes and the Baltic Sea are much smaller. Phylogenomic analysisand ancestral state reconstruction showed that approximately half of the brackishMAGs had freshwater ancestors and half had marine ancestors. Phylogeneticdistances were on average shorter to freshwater ancestors, but when subsampling thetree to the same number of freshwater and marine MAG clusters, the distances werenot significantly different. Brackish genomes belonging to Acidimicrobiia,Actinobacteria and Cyanobacteriia tended to originate from freshwater bacteria, whilethose of Alphaproteobacteria and Bacteroidia mainly had evolved from marinebacteria.
Mikroorganismer spelar avgörande roller i akvatiska ekosystem där de driverkretsloppen av näringsämnen. En ökad förståelse för hur mikroorganismer anpassarsig till miljöförändringar är viktigt för att förutsäga hur akvatiska ekosystem kommeratt förändras som en konsekvens av global uppvärmning, och sådan förståelse kanuppnås genom att studera tidigare skeenden i evolutionen. I detta projekt undersökervi det evolutionära förhållandet mellan brackvatten-bakterier från Östersjön ochKaspiska havet med sötvattens- och marina bakterier, med målet att förstå hurbrackvatten-bakterier har utvecklats. 11,276 bakteriella arvsmassor somrekonstruerats med metagenomik från sju data-set användes för att utföra enjämförande analys av bakterie-genom från söt-, brack och havsvatten. Klustring avgenomen baserat på parvis genomsnittlig nukleotididentitet (ANI) på ungefärligartnivå (96,5% ANI), grupperade Östersjöns bakterier tillsammans med Kaspiskahavets bakterier mer än med bakterier från svenska sjöar, trots att det geografiskaavståndet mellan svenska sjöar och Östersjön är mycket mindre. Fylogenetisk analysvisade att ungefär hälften av brackvatten arterna hade anfäder från sötvatten ochhälften från havsvatten. De fylogenetiska avstånden var i genomsnitt kortare tillanfaderna i sötvatten, men när man reducerade trädet till att ha samma antal sötvattenoch marina arter var avstånden inte längre signifikant olika. Brackvatten-arter somtillhörde Acidimicrobiia, Actinobacteria och Cyanobacteriia tenderade att härstammafrån sötvattenbakterier, medan de från Alphaproteobacteria och Bacteroidia främsthärstammade från marina bakterier.

Telomeres, the protective caps at the ends of all vertebrate chromosomes, naturally undergo changes in length. These changes in telomere lengths may be a “molecular clock” by providing a counting mechanism of DNA replication events. In populations of jawed vertebrates (gnathostomes), telomere length has been shown to change with age; and thus measurements of telomere lengths may provide a novel means of determining the ages of free-living animals. Determinations of the age structure of populations of aquatic vertebrates (teleosts, chondrichthyans and marine mammals) are vital for sustainable management and conservation efforts. Yet, the commonly applied increment based ageing techniques are limited by the subjectivity of increment patterning and destructive sampling. I aimed to assess the application of telomere length as an age determinate for populations of aquatic vertebrates and to evaluate the biological implications and evolutionary origins of this trait amongst the gnathostomes. Telomere length change with age was investigated in an exemplar chondrichthyan, teleost and marine mammal species, to determine whether aquatic gnathostomes share the general pattern of declining telomeres with age, as found in terrestrial mammals. Chapter Two provides the first assessment of telomere length change with age in a chondrichthyan species, the Port Jackson shark. Four types of tissues from Port Jackson sharks, ranging in age from 0 to 17 years, were sampled and telomere length were estimated using three measurement methods: (i) relative quantitative PCR (qPCR); (ii) absolute qPCR; and (iii) the terminal restriction fragment (TRF) analysis. No relationship between telomere length and age was found for any of the tissues, using any method. In Chapter Three, telomere length was measured in specimens of the common carp from two tissues using the absolute qPCR method. Telomere length measurements were then correlated with ages estimated from otolith increment counts and length-at-age calculations. Measurements of telomere length were highly variable in both muscle biopsies and fin clips; however, telomeres from muscle biopsies significantly increased in length – in contrast to the more generalised pattern of telomere length attrition and marking the second reported case of an increase in telomere length with age in vertebrates. In terrestrial mammals telomere shortening is negatively correlated with donor age. In Chapter Four, I tested whether this pattern of declining telomere lengths was found in a pinniped species, the Australian sea lion. Telomere lengths were measured in flipper clips from specimens by absolute qPCR and compared between three age classes: pups, juveniles, and adults. Mean telomere lengths of the adults were significantly smaller than the juvenile and pup classes confirming that the Australian sea lion shares the general mammalian pattern of telomere length attrition. Relationships between the rate of telomere length change with age and species longevity have been observed in birds and mammals, suggesting that the rate of telomere length change is an informative measure of ageing. In Chapter Five, using a data set of 20 teleost and chondrichthyan species, I tested whether fishes showed a similar pattern. I found that the rate of telomere length change with age is significantly different between species of fishes and that these rates of change are inversely correlated with longevity. The findings of Chapters Two, Three & Four indicated that telomeres do not provide a suitable means of determining the ages of individuals and at best are limited to assigning broad age classes. This is largely due to the high degree of variability of telomere lengths between individuals within all age classes. In addition, these Chapters (2, 3 & 4) also highlight that patterns of telomere length change with age are highly variable within the gnathostomes; and thus, telomere length change cannot be characterised by a single pattern for all lineages. In fact, three patterns of telomere length change with age in the gnathostomes were found: (i) declining telomere lengths; (ii) increasing telomere lengths; and (iii) no significant change in telomere length with age. However, identifying the selective factors responsible for the assignment of patterns of telomere length change is hampered by a lack of the understanding of the evolutionary origins of these patterns. Therefore, in Chapter Six I sought to outline the phylogenetic distribution of patterns of telomere length change with age in the gnathostomes to determine the evolutionary origin(s) of this trait. Two alternative hypotheses for the evolution of telomere length change were tested by ancestral state reconstruction in a set of 40 gnathostomes, for which I have significantly expanded the sampling of chondrichthyans and teleosts. The most likely/parsimonious pattern of telomere length change in the common gnathostome ancestor suggested that telomere length change with age was not present ancestrally and has since evolved independently. I was also able to elucidate the evolutionary history of transitions to and between the three patterns of telomere length change within the available gnathostome lineages, with the birds and teleosts displaying the highest rates of evolutionary lability of patterns of telomere length change with age. The macro-evolutionary analysis (Chapter 6) identified relatively rapid evolutionary patterns of telomere length change with age in two gnathostome clades. However, as highlighted by the variability of telomere lengths among individuals within all age classes, furthering an interpretation of the causes and consequences of variable patterns of telomere length change will require a focus at the species level and a shift to following individuals through out their lifetime.
Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2010

AbstractSunzi said, “Warfare is pivotal to the state. [It is] a milieu where life and death are decided, [it holds] the path to survival or extermination and cannot be neglected.” In like manner, the Commentary of Zuo (Zuozhuan) states, “Rituals and warfare are of vital importance to the state.” From this we see that besides ritual matters, such as ancestor worship and maintaining the temples, rulers in ancient China considered warfare and military training to be of utmost importance. Consequently, much attention was paid to sacrificial implements and weapons of war. The production and maintenance of arms was an integral part of this effort as it impacted state security as a whole. The study of ancient arms therefore not only teaches us about ancient weaponry and methods of combat but also yields unique insights into the technology and organization of war. The principal short-range weapons during the Han dynasty were jian (double-edged sword)and dao (single-edged sword), while the latter gradually replaced the jian in military use as the dynasty wore on, partly as a result of the rise of cavalry. This paper contains three parts: iron smelting and weapon production in the Han dynasty; the ancient techniques of iron smelting in shaft furnace; and reconstructing the Han ring-pommel dao with ancient methods.

This chapter investigates Reconstruction theology by demonstrating that the idea of nature played other roles in the quest to save humanity's proper place in God's hierarchical creation, such as through the religious community's construction of Christian nationalism. During the 1970s, religious communities built a unique history of the United States by making their faith a primary reason for the success of the country. The chapter highlights the idea of humanity as a creation of God and the idea of earth's wilderness as the realm where humans were meant to dominate, but not abuse. The chapter discusses politically conservative evangelicals who depicted the unconquered forests of North America as healthy obstacles, which encouraged “real Americans” of the past to conform to their God-ordained, gender-specific family norms. It describes the struggle with the wilderness that politically conservative evangelicals believed their religious ancestors gained ownership of the land, which became the United States.

<em>Abstract</em>.-We develop the view, based on life cycle differences and recently published sister group relationships, that the freshwater life cycle was the ancestral character state leading to anadromy among salmoniforms, whereas the marine life cycle was the ancestral character state leading to anadromy among osmeriforms. In contrast to most salmonid fishes, the reproductive migrations of smelts are generally characterized by brief excursions to spawn in freshwater, and larvae may spend no more than 24 h in freshwater before being transported to coastal marine or estuarine environments. We reconstructed the phylogeny of the suborder Osmeroidei to establish the phylogenetic relationships among anadromous, marine, and freshwater species of this taxon. We mapped these life cycles onto phylogenetic trees of osmeriforms and salmoniforms and applied character-reconstruction methodology based on simple parsimony and likelihood methodologies. A freshwater origin of salmonids was supported by our analyses, whereas either marine or anadromous life cycles characterized the evolution of osmeroids. The possibility that the evolution of anadromy in salmonids and osmeroids followed separate paths requires a reconsideration of some generalizations concerning anadromy. We hypothesize that anadromy in osmeroids may be first and foremost an adaptation to place embryos and the early larval stages in reproductive safe sites to maximize their survival. The evolution of exclusive freshwater species of osmeriforms has occurred via anadromy through the various processes associated with landlocking. Freshwater amphidromy in osmeroids is most likely a consequence of anadromy rather than a precursor and may be contingent upon the availability of food resources in freshwater. Finally, marine osmeroids have been derived from anadromous ancestors and are "safe-site" specialists, exploiting principally the upper intertidal zone for reproduction. We also suggest that such contrasting evolutionary pathways to anadromy may provide insight into the evolution of partial migration, observed uniquely in salmonids, and the nature and extent of population genetic structure found in the two groups of fishes.