39 research outputs found

    CA✩ Forum on Theory in Anthropology The Animal Connection and Human Evolution

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    A suite of unique physical and behavioral characteristics distinguishes Homo sapiens from other mammals. Three diagnostic human behaviors played key roles in human evolution: tool making, symbolic behavior and language, and the domestication of plants and animals. I focus here on a previously unrecognized fourth behavior, which I call the animal connection, that characterized the human lineage over the past 2.6 million years. I propose that the animal connection is the underlying link among the other key human behaviors and that it substantially influenced the evolution of humans. The evolution of any species can be understood by first identifying unique or diagnostic characteristics of the modern species and then tracing their development through time. Traits that are ancient and continuous and that provide causal explanations for significant attributes of the species in question are likely to have played crucial roles during evolution. Traits often considered diagnostic of humans and significant in their evolution are (1) making and using tools (Darwin 1871; The animal connection comprises an increasingly intimate and reciprocal set of interactions between animals and humans (i.e., members of the genus Homo) starting ∼2.6 million years ago (mya). The animal connection began with the exploitation and observation of animals by humans. Over time, regular social interactions were incorporated into the animal connection. This trait is expressed today in the widespread Pat Shipman is Professor of Biological Anthropology in the Department of Anthropology of Pennsylvania State University (University Park, Pennsylvania 16802, U.S.A. [[email protected]]). This paper was submitted 3 X 08 and accepted 23 VII 09. adoption, or cross-species alloparenting, of animals-including dingoes, possums, bandicoots, raccoons, deer, moose, bison, fruit bats, lizards, bears, tapir, monkeys, sloths, coatimundis, antelopes, zebra, tree kangaroos, rabbits, weasels, ferrets, rodents, and birds, cervids, felids, and canids of all types (Serpell 1989)-as members of the family. This adoption involves active nurturing and care; ethnographic studies and early travelers' accounts often report women breast-feeding young animals or prechewing food for them (e.g., Galton 1865; Tool Making and Tool Using Tool making and tool using are much more complex behaviors in humans than in other animals. Humans make a vast array of tools and have made tools for ∼2.6 million years (m.yr.; Early humans used stone tools repeatedly for carcass processing. Direct evidence of this function comes from cut marks, scraping marks, and percussion scars on bones from many different sites (e.g., Blumenschine 1995; Tool using in the broad sense is an extrasomatic adaptation (White 1959) of humans: a means by which humans evolved behaviorally without adapting physically. Tool use is a predominant, universal, and daily aspect of present human life, implying that the adaptive advantage of tools has been greater to humans than to apes. Among nonhuman mammals, tool use is less complex and less frequent. Modern chimpanzees are the most adept animal tool makers and produce the largest tool kit. Chimpanzees make and use nests; termiting or anting implements; leaf sponges; hammerstones and anvils for breaking nuts; and sticks to pick marrow from bones, to dig for underground storage organs (e.g., tubers), and to locate and extract bush babies from tree hollows (e.g., Captive but not wild bonobos make flaked stone implements The importance of tool use in chimpanzees varies. Chimpanzees at Mahale spend little time ant fishing (∼1%-2% of the daylight hours) and gain little food (0.6 g protein; Nishida and Haraiwa 1982). However, Taï chimps spend hours cracking nuts and gain as much as 3,000 calories/day in season. Excluding nut cracking, Taï chimpanzees use a tool only every second day Significantly, humans use tools for different purposes than do nonhuman primates. Ape tools are rarely involved in killing or obtaining meat (Stanford 1996; Symbolic Behavior Following others Language, specifically, is widely considered a primary hallmark of humanity (e.g., Language differs from other types of communication by its symbolic and reflective content, using arbitrary symbols (words) to convey meaning (Pinker and Jackendoff 2005). Language today involves syntax, grammar, lexical items (which refer to concrete objects, perceptible attributes, or actions), and disambiguators or grammatical items that permit humans to express complex relational or referential ideas and to speak of the past, the present, the future, and the hypothetical Wild animals demonstrably communicate with each other. Vervet monkeys give different alarm calls to signal aerial versus terrestrial predators (Cheney and Seyfarth 1990). The symbolic vocabulary is clearly shared by the audience (the social group). However, the topic is not "snake" but "danger-snake"; the call cannot be used to ask the color of the snake, for example. Animals in experimental situations are capable of fairly sophisticated communication. Educated apes use about 400 words, do not use syntax or grammar, and do not combine more than two or three words into sentences (Savage-Rumbaugh and Lewin 1994). One of the most linguistically adept nonhumans, Kanzi the bonobo, uses fewer than 400 words (lexigrams) but understands about 3,000 Domestication Central to understanding the Neolithic Revolution Domestication itself is a process in which selective breeding by humans produces genetic change in a target species (Bö-könyi 1989; Only after fixation of behavioral traits are the morphological changes selected for, making the onset of domestication difficult to recognize. At the heart of the process of taming a wild animal, bringing it into the household, and controlling its reproduction and genetic output over generations is the formation of an intimate, reciprocal, and individual relationship between a particular animal and a particular human (Clutton-Brock 1999). Forming a relationship with an animal is more akin to negotiating a partnership than to caretaking a plant The ease with which zoonoses spread from domestic animals to humans shows the biological intimacy of the animal connection. In the archaeological record, domestic plants are recognized by changes in seed morphology, by appearance in new geographic regions, and/or by genetic analysis. The apparatus of agriculture, such as ploughs, hoes, scythes, granaries, fields, fences, or irrigation ditches, leaves archaeologically visible traces. Other mammals are not known to domesticate plants or animals. The Animal Connection as a Diagnostic Trait Like the traits reviewed above, the animal connection is universal among humans, is capable of powerfully transforming behavior, and is absent or extremely rare among other species. Same-species alloparenting is reasonably common among nonhuman primates Numerous reports allege cross-species alloparenting of young humans by wild animals. Purported alloparents include wolf, bear, dog, gazelle, chimpanzee, vervet monkey, goat, sheep, cow, ostrich, jackal, panther, and leopard. Few written reports of feral children raised by other mammals The Hypothesis I hypothesize that as an ancient, diagnostic trait of the human lineage, the animal connection had a major influence on human evolution, genetics, and behavior. This hypothesis predicts that the fossil and archaeological record will include abundant evidence that (1) humans were intimately and persistently connected with animals, (2) human adaptive changes were causally linked to the animal connection, and (3) a meaningful adaptive advantage of the animal connection can be identified in each stage of human evolution. Below, I review the archaeological and fossil record in three broad chronological stages and discuss evidence related to my hypothesis. I focus on the following key adaptive transformations: the origin and evolution of tool making, the manipulation of symbols and origin of language, and the domestication of animals and plants

    Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

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    Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

    Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

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    Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

    Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

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    This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

    Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

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    Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

    Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types

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    Protein ubiquitination is a dynamic and reversibleprocess of adding single ubiquitin molecules orvarious ubiquitin chains to target proteins. Here,using multidimensional omic data of 9,125 tumorsamples across 33 cancer types from The CancerGenome Atlas, we perform comprehensive molecu-lar characterization of 929 ubiquitin-related genesand 95 deubiquitinase genes. Among them, we sys-tematically identify top somatic driver candidates,including mutatedFBXW7with cancer-type-specificpatterns and amplifiedMDM2showing a mutuallyexclusive pattern withBRAFmutations. Ubiquitinpathway genes tend to be upregulated in cancermediated by diverse mechanisms. By integratingpan-cancer multiomic data, we identify a group oftumor samples that exhibit worse prognosis. Thesesamples are consistently associated with the upre-gulation of cell-cycle and DNA repair pathways, char-acterized by mutatedTP53,MYC/TERTamplifica-tion, andAPC/PTENdeletion. Our analysishighlights the importance of the ubiquitin pathwayin cancer development and lays a foundation fordeveloping relevant therapeutic strategies

    The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

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    Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.

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    Cancer progression involves the gradual loss of a differentiated phenotype and acquisition of progenitor and stem-cell-like features. Here, we provide novel stemness indices for assessing the degree of oncogenic dedifferentiation. We used an innovative one-class logistic regression (OCLR) machine-learning algorithm to extract transcriptomic and epigenetic feature sets derived from non-transformed pluripotent stem cells and their differentiated progeny. Using OCLR, we were able to identify previously undiscovered biological mechanisms associated with the dedifferentiated oncogenic state. Analyses of the tumor microenvironment revealed unanticipated correlation of cancer stemness with immune checkpoint expression and infiltrating immune cells. We found that the dedifferentiated oncogenic phenotype was generally most prominent in metastatic tumors. Application of our stemness indices to single-cell data revealed patterns of intra-tumor molecular heterogeneity. Finally, the indices allowed for the identification of novel targets and possible targeted therapies aimed at tumor differentiation

    Molecular characterization and clinical relevance of metabolic expression subtypes in human cancers.

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    Metabolic reprogramming provides critical information for clinical oncology. Using molecular data of 9,125 patient samples from The Cancer Genome Atlas, we identified tumor subtypes in 33 cancer types based on mRNA expression patterns of seven major metabolic processes and assessed their clinical relevance. Our metabolic expression subtypes correlated extensively with clinical outcome: subtypes with upregulated carbohydrate, nucleotide, and vitamin/cofactor metabolism most consistently correlated with worse prognosis, whereas subtypes with upregulated lipid metabolism showed the opposite. Metabolic subtypes correlated with diverse somatic drivers but exhibited effects convergent on cancer hallmark pathways and were modulated by highly recurrent master regulators across cancer types. As a proof-of-concept example, we demonstrated that knockdown of SNAI1 or RUNX1—master regulators of carbohydrate metabolic subtypes-modulates metabolic activity and drug sensitivity. Our study provides a system-level view of metabolic heterogeneity within and across cancer types and identifies pathway cross-talk, suggesting related prognostic, therapeutic, and predictive utility

    Freed to Fly Again

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