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In a separate and subsequent analysis, three additional taxa (genomes of the horseshoe crabs , , and ) were added to the taxa in the principal OMA run, with all other procedures as specified above.

From the output of the OMA analysis of six arthropod genomes, we extracted a subset of orthogroups wherein exactly two spider paralogs were present for one ortholog (i.e., 1:2 orthology). was chosen as the reference genome in comparative analyses both for the quality of its assembly and for its archetypal gene content among Arthropoda. Gene trees for this subset of orthogroups were inferred to examine the topological relationship between homologous sequences of arachnopulmonate and non-arachnopulmonate taxa. These orthogroups were aligned using MUSCLE v.3.8 [ 122 ] and ambiguously aligned regions were culled using GBlocks v.0.91b [ 123 ] using the commands –b3 = 8 (maximum of eight contiguous non-conserved positions), –b4 = 10 (minimum of ten positions in a block), and –b5 = h (gap positions allowed for a maximum of half the sequences). Maximum likelihood analyses were conducted using the LG + Γ model with four rate categories [ 124 , Cheap Big Discount Classic For Sale MultiWear Wrap Day Lily by VIDA VIDA p0ieFq
] and 500 independent starts in RAxML v. 7.3.0 [ 126 ].

We characterized whether the resulting tree topologies corresponded to Hypothesis 1 (common duplication in the most recent common ancestor (MRCA) of spiders and scorpions), Hypothesis 2 (lineage-specific duplication events in each of spiders and scorpions), an indeterminate tree topology (corresponding to neither scenario, typically due to the non-monophyly of the outgroup taxa), or an uninformative tree topology (due to the lack of any scorpion paralogs). Cases where the two spider paralogs formed a grade with respect to a single scorpion paralog were additionally classified as partially congruent with Hypothesis 1. The set of gene trees either partially or fully congruent with Hypothesis 1 is henceforth termed “Tree Set 1”. Alignments and gene tree files are available on request.

To infer the relationship between arachnopulmonate and xiphosuran paralogs, from the OMA analysis of nine genomes (the six genomes above, , , and ) we separately extracted another subset of orthogroups, wherein two, three, or four horseshoe crab paralogs from any of the three horseshoe crab genomes were detected for one ortholog (i.e., 1:2, 1:3, or 1:4 orthology). We inferred gene trees with the approach specified above. We again distinguished two scenarios, namely (1) separate WGD events in the MRCA of Arachnopulmonata and Xiphosura (Hypothesis 3), and (2) a common WGD event in the MRCA of all Chelicerata (Hypothesis 4). Cases where ancient paralogy was detected in Xiphosura alone (and not Arachnopulmonata) were classified as partially congruent with Hypothesis 3. The set of gene trees either partially or fully consistent with Hypothesis 3 was termed “Tree Set 2”. Alignments and gene tree files are available on request.

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, which make further study and the division of cognitive labor possible.

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Conceptualization is a method of expanding man’s consciousness by reducing the number of its content’s units—a systematic means to an unlimited integration of cognitive data.

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It is crucially important to grasp the fact that a concept is an “open-end” classification which includes the yet-to-be-discovered characteristics of a given group of existents. All of man’s knowledge rests on that fact.

“The Cognitive Role of Concepts,” , 66

Concepts and, therefore, language are a tool of cognition— of communication, as is usually assumed. Communication is merely the consequence, not the cause nor the primary purpose of concept-formation—a crucial consequence, of invaluable importance to men, but still only a consequence. ; the necessary precondition of communication is that one have something to communicate ....

The primary purpose of concepts and of language is to provide man with a system of cognitive classification and organization, which enables him to acquire knowledge on an unlimited scale; this means: to keep order in man’s mind and enable him to think.

“The Cognitive Role of Concepts,” , 69

Abstract ideas are conceptual integrations which subsume an incalculable number of concretes—and ... without abstract ideas you would not be able to deal with concrete, particular, real-life problems. You would be in the position of a newborn infant, to whom every object is a unique, unprecedented phenomenon. The difference between his mental state and yours lies in the number of conceptual integrations your mind has performed.

“Philosophy: Who Needs It,” , 5

Conceptual awareness is the only type of awareness capable of integrating past, present and future. Sensations are merely an awareness of the present and cannot be retained beyond the immediate moment; percepts are retained and, through automatic memory, provide a certain rudimentary link to the past, but cannot project the future. It is only conceptual awareness that can grasp and hold the total of its experience—extrospectively, the continuity of existence; introspectively, the continuity of consciousness—and thus enable its possessor to project his course long-range.

“Axiomatic Concepts,” , 57

There are many special or “cross-filed” chains of abstractions (of interconnected concepts) in man’s mind. Cognitive abstractions are the fundamental chain, on which all the others depend. Such chains are mental integrations, serving a special purpose and formed accordingly by a special criterion.

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