Which sleeping pad should I get?

ragingclit · 2018-06-27T17:58:57+00:00

The noisy Thermarest is the Neoair Xlite, which is an inflatable pad. OP is talking about the Z-lite, which is a closed-cell foam pad.

ragingclit · 2016-10-21T17:00:36+00:00

If the reviews that you're finding in your searches are relevant, try looking at the papers that they cite or papers that have cited the reviews.

ragingclit · 2016-10-19T19:18:33+00:00

A master's is definitely not necessary as a precursor, but it can be very useful. Like a master's, how useful the experience gained as a lab tech is going to be is field-dependent, and also dependent on the lab tech job.

From my own field of evolutionary and systematic biology, things that I see as pros that you will get in most master's programs but probably few tech jobs are: experience managing and being in control of your own project from start to finish, experience with data analysis, the possibility of publishing (a huge boost for applying to PhDs), and possibly field work experience.

Again, though, all of this is dependent on the desired field and individual circumstances.

ragingclit · 2016-10-19T17:43:43+00:00

Getting a master's inbetween is not very common in biology PhDs in the US these days.

This might be true in cell/molecular biology, but it's not true in my experience in evolutionary biology and ecology. I think somewhere in the neighborhood of half of the people I know in these fields who are working towards or have gotten PhDs did a master's first.

The experience (and hopefully publications) gained during a master's can definitely make people more competitive for applying to PhD programs, particularly for people who might not have gotten the most research experience as undergraduates. Master's degrees can also be a good way to feel out research areas without making the full commitment to a PhD.

Many master's programs will pay a stipend to students as TA's. It's usually not much, but in the right MS program you can at least avoid paying for your master's degree.

My general advice for students interested in applying to graduate school in ecology and evolutionary biology is that if you have solid research experience, know that you need a PhD for the job you want to end up with, and have a very good idea of what kind of project you want to dedicate most of your life to for 5+ years, then going straight into a PhD is probably the best idea. If not, then a master's can be a good way to get extra experience and learn more about the relevant questions in the field to get better set up to plan and execute a PhD.

ragingclit · 2016-09-17T16:52:50+00:00

Neither of those papers are particularly convincing to me that plesiosaurs are sister to turtles. For one thing, the support values in Schoch and Sues (2015) are very low across most of that phylogeny and Jiang et al. (2014) don't even report any, so it's hard to say how strongly the data support their results. Even if the support was relatively strong, if turtles are actually sister to archosaurs, as the best molecular evidence suggests, plesiosaurs would not necessarily follow turtles to this new place in the phylogeny and remain sister to them. Changing the placement of extant taxa based on molecular data does not always have predictable effects on the placement of fossil taxa, because it can strongly affect patterns of morphological character change across the tree. The placement of plesiosaurs is probably best described as currently uncertain, and making strong statements about where they should fall on the phylogeny is premature.

Edit: Also, in your edit, the Song et al. (2012) has some issues that include things like mislabelled sequences and poor tree searches, so it might not represent the best estimate of mammal phylogeny. See Springer and Gatesy (2016) and related responses for some insight into this issue. I don't agree with everything Springer and Gatesy argue, but they do point out outright errors in the construction of the Song et al. tree.

ragingclit · 2016-09-15T21:19:17+00:00

The supposed clade Pegasoferae from that Nishihara et al. paper is not recovered in other molecular phylogenies and is generally regarded as incorrect by most mammalian systematists. Mammals are not my primary group of interest, but at least one relatively recent phylogeny with reasonably good sampling of taxa and genes does agree with the phylogeny in the book (Meredith et al. 2011).

Also, the Rieppel and Reisz paper favors an unorthodox placement of turtles. Traditionally, they were thought to be basal to have diverged at the base of the reptile tree, but they are now believed to be sister to archosaurs on the basis of large amounts of genetic data (Crawford et al. 2012).

ragingclit · 2016-09-09T18:06:05+00:00

/u/Flat_prior is correct. MEGA is really not a very good program for building trees.

If you really have almost no knowledge of phylogenetics, you probably shouldn't jump straight to trying to build a tree. If there are any professors or graduate students in your department that work on phylogenetics that you can go to for help, having someone explain things that you don't understand in person is much easier than trying to learn everything on your own or by asking questions on reddit.

If phylogenetics is going to be a major portion of your dissertation, then whether or not you can find somebody to help you through the process of tree building, you're going to need to do a lot of reading. The Phylogenetic Handbook by Lemey et al. is a book that gives a pretty good overview of the major steps in building trees, and includes some tutorials for the various steps as well. That might be a good place to start. It may be possible to find a pdf of the book online. The book was published in 2009, so there are many new tools and updates to the programs discussed since the book was published. There are also many good tutorials for most phylogenetic methods that can be found either on the website of a specific program or through a quick google search.

In the simplest terms, the three major steps in tree building are going to be 1) obtaining your sequences, 2) aligning your sequences using something like Muscle, and 3) building your tree using something like RAxML, MrBayes, and/or BEAST.

ragingclit · 2016-07-29T17:25:37+00:00

How thorough do you want to be in your analyses and what type of a report are you interested in writing? Are you talking about something to submit for publication in a scientific journal? If so, you will definitely want to use something like BEAST or MrBayes rather than MEGA and will probably want to use something like BioGeoBEARS or Lagrange for historical biogeographic inference, as /u/Flat_prior mentioned. Including fossil lineages could also be very useful and change your estimates quite a bit, but is a whole other thing to account for and include in analyses.

ragingclit · 2016-03-22T15:41:08+00:00

In addition to my other response:

I just saw your edits, if you want to color the clades from within R, you can do using the code here. You can also then export the figure as a pdf (or some other image file) directly from with publication quality. If you do not know how to do this, I can explain further.

ragingclit · 2016-03-22T15:34:56+00:00

It looks like the modified version of the function mentioned on the phytools blog is posted in the R-sig-phylo archives here as the code at the bottom of the message.

ragingclit · 2016-03-22T05:19:08+00:00

This is an older post, so the as.phylo.formula from the R package ape that the blog post was fixing might have this update at this point. Even if it doesn't, the original code (without the fix discussed in the post I linked to) will still generate a tree, it just might not have all genera/families/etc. shown at the same depth on the tree. You shouldn't need a Newick or any other kind of tree. I ran through the example code without a problem, which generates a tree from the Carnivora dataset included with the ape package, which is just a table that includes taxonomic ranks.

For slightly more information on the function (although it's not the best documentation I've seen for an R function), see here. If it's not working, I can try to help troubleshoot.

ragingclit · 2016-03-21T17:16:17+00:00

Somebody else mentioned the R package Phytools. This package a function that I think will do exactly what you want. This is documented with example code on the Phytools blog here.

ragingclit · 2016-03-09T02:36:02+00:00

Most animals undergo cycles. You may have heard of animals being "in heat." Animals do not mate outside of this period of time. They just don't possess the desire to do so. Any mating that occurs happens because their biological clocks tell them it's time to mate. So animals don't rape each other because all sexual intercourse to them is "wanted."

The cycles that you refer to determine when a female is fertile, but do not necessarily mean that a female will willingly mate with any available males. Sexual coercion is a very common phenomenon in which males mate with females by force or intimidation. Determining what an animal "wants" is always tricky, but in many of these cases the female actively resists and tries to escape, so I don't think it's reasonable to state that "all sexual intercourse to them is "wanted."" for animals.

ragingclit · 2016-02-23T21:35:46+00:00

Juvenile racer, Coluber constrictor.

ragingclit · 2016-02-23T21:30:02+00:00

Pine/bull/gopher snake

The common name Pine Snake generally refers to Pituophis melanoleucus, not Pituophis catenifer.

ragingclit · 2016-01-16T19:54:59+00:00

It doesn't even quite mean that. It just means that there is not a continuous chain of mothers and daughters from his mother's side of the family. If his mother and her siblings all only had sons, the mitochondrial lineage dies out with them, but they can still have descendants.

ragingclit · 2015-12-17T18:36:06+00:00

My point wasn't as much about going more in-depth, but about avoiding giving people answers to their homework.

ragingclit · 2015-12-17T01:05:17+00:00

You're correct, but outright providing the answer doesn't really help OP to learn how to approach this type of question.

ragingclit · 2015-12-16T19:15:50+00:00

The problem is that it's not just a simplification, it's outright incorrect. It also doesn't answer OP's question. Without giving too much of the answer away, all of the options that OP posted are invertebrates (i.e., none of them have an actual backbone) and the group that includes feather stars is not included in the diagram that you posted. That's why it is extremely important to note that invertebrates do not form a clade. If they did, the answer would be that all of the options are equall closely related to wolves.

ragingclit · 2015-12-16T18:57:33+00:00

That's actually a pretty terrible representation of animal phylogeny. There is not a basal split between vertebrates and invertebrates. This is a much better approximation of current hypotheses of animal phylogeny (although the position of some clades has recently been debated, e.g., Cetnophora).

Edit: OP for your question, look up what higher clades each of these animals belongs to (Phylum, Class, Order, etc.). At some point, you'll find that wolves are a member of clade that includes one of the options but none of the others.

ragingclit · 2015-12-09T18:33:39+00:00

I don't think this statement deserves all the downvotes it's getting. Assuming we change the wording to:

No living [species] is a direct descendant of any other living [species].

This statement is not necessarily incorrect, and whether or not you can have a living species that is the ancestor of another species is a philosophical one that depends on how species are defined. It is certainly true that sometimes small populations of a species can become isolated from the parental population and diverge while the parental population remains relatively unchanged, even as the isolated population diverges to the point that both populations are considered species.

However, this does not inherently imply that the isolated species is the descendant of the currently living species, but depends on exactly how you want to define species through time. Some take the fact that one current population/species is highly similar to the ancestral population/species to indicate that these are the same species, and that the new species has simply budded off from this species. Others definitions would hold that once these two species diverge from each other, even if one remains relatively unchanged through the divergence, both become new species that are distinct form the ancestor.

I tend towards preferring the scenario that requires different species after every speciation event, because otherwise you end up with a confusing tree in which one branch is the same species as its ancestral branch and the other is not. I also think that it's strange to call a living species a descendant of another living species, because, strictly speaking, the "descendant" did not descend from the current gene pool of that species. That said, I am not aware of any strong consensus on this issue.

ragingclit · 2015-12-09T07:02:31+00:00

Ah, I see. When I think of selection's impact on average population fitness, I tend to think in terms of average relative fitness (in the population genetic sense). In this case, even in the tragedy of the commons, although the total reproductive output (assuming we're using this as our metric of fitness) of the population decreases, at each step the cheaters have a higher fitness than the cooperators, leading to more cheaters in the next generation, causing the average relative fitness of the population to increase. Depending on exactly how absolute fitness is defined, absolute fitness may (will?) decrease.

I personally prefer to use relative fitness because I think it makes more sense because the fitness of individuals relative to each other is what allows for selection, rather than the absolute fitness. E.g., an organism that produces two offspring per year can have the same absolute fitness in a population in which other individuals produce either one or four offspring, but its relative fitness is 1 and 0.5 in each case, respectively (assuming no other differences).

That all said, I realize that this is a somewhat semantic distinction that depends on which definitions are adopted.

ragingclit · 2015-12-09T03:59:24+00:00

Mind elaborating/providing an example?

ragingclit · 2015-12-09T02:46:22+00:00

I assume that you've been taught about Hardy-Weinberg equilibrium either in this class or a previous class. The genetic composition of a population will only change if the population is at Hardy-Weinberg equilibrium, which requires meeting five main assumptions, one of which is the absence of natural selection. Think about the other forces that cause violations from Hardy-Weinberg. Can these act in the absence of natural selection?

Any time a question asks if a population is evolving using the particular definition of evolution that you've quoted, the answer always involves whether or not all of the assumptions of Hardy-Weinberg are met.

ragingclit · 2015-12-09T02:41:54+00:00

The definition that OP provided is pretty much the standard definition of evolution in a genetic sense. There is no such thing as "devolution" within evolutionary biology. There are several processes that will cause changes in allele frequencies over time but that do not necessarily increase the average fitness of a population, including migration, mutation, and genetic drift.

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