Molecular Clock Hypothesis Worksheet

QUESTION 1

According to the molecular clock hypothesis, biological sequences undergo mutations at a rate thathas decreased linearly since the beginning of life on earthhas increased linearly since the beginning of life on earth has remained constant through the history of life on earchhas increased exponentially since the beginning of life on earth 

1. QUESTION 2

Which of the following is a tree-building method described in the textbook to construct a phylogenetic tree?neighbor-joining methods, like UPGMAbash methods, like ls, cd, and lessNussinov-Jacobson algorithm SNP calling methods, such as GATK

QUESTION 3

Ryan et al. writes:Appropriate Hox expression is required to confer the appropriate regional identity upon these Hox-expressing body regions — ergo, a Hox code.
Which statement best describes the way in which Hox expression confers regional identity to pattern the primary body plan in a single individual human, for example? paralogous Hox genes within a genome are expressed in different regions along the primary body axis, over the course of developmentorthologous primate-specific Hox genes are expressed in different regions along the primary body axis, over the course of development, in a pattern that is unique to primatesisoforms of a single ancestral Hox gene are expressed in different regions along the primary body axis over the course of developmentisoforms of a human-specific Hox genes are expressed in different regions along the primary body axis over the course of development

QUESTION 4

In Ryan et al., a phylogenetic analysis of Hox genes in Nematostella and other animals is performed. Which statement best describes the final alignment used in the presented phylogenetic analyses?The alignment includes many small gaps that represent insertion and deletion events in the homeodomain and neghboring conserved domains.The alignment contains the complete sequence of each putative Hox gene.The alignment only contains a portion of each gene: the homeodomain. The alignment contains large gapped regions that represents entire domains that have been inserted or removed to the putative Hox genes.

QUESTION 5

Consider Figure 2. in Ryan et al. Which Hox genes are missing in Nematostella? Why are these genes missing, according to the hypothesis presented in Figure 2? Cnidarians contain orthologs of all Hox genes found in Bilaterians, according to orthology.Central Hox genes (i.e. Hox4–Hox8) are missing. Each of these genes was independently lost from the Cnidarian lineage.Central Hox genes (i.e. Hox4–Hox8) are missing.  The ancestor of the central hox genes was lost from Cndiarians before the subsequent gene duplication events leading to muliple central hox genes in Bilaterians.Central Hox genes (i.e. Hox4–Hox8) are missing, because hox genes evolved in Bilateria after the divergence with Cnidarians.

QUESTION 6

Which command flag in iqtree specifies the input alignment file?QUESTION 1

Many unique features of nonbilaterian animals are currently unknown to us: a ‘hidden biology’.Nonbilaterian animal biology includes novel mechanisms that underlie structures and functions that are shared with bilaterians. All nonbilaterian animals’ biology can be studied as a subset of bilaterian biology.Nonbilaterian animals have novel structures and functions, facilitated by novel mechanisms, that are not found in bilaterian model species.
Bilaterians are more advanced than all other animals.

QUESTION 2

Ctenophora (comb jellies)PlacozoaCnidariaPorifera (sponges)BilateriaChoanoflagellatea (choanoflagellates)

QUESTION 3

“Where is my mind? How sponges and placozoans may have lost neural cell types””Losing complexity: the role of simplification in macroevolution””Getting nervous: an evolutionary overhaul for communication””The hidden biology of sponges and ctenophores””The role of cnidarian developmental biology in unraveling axis formation and Wnt signaling”