What ways are there to determine how big genera are?

What ways are there to determine how big genera are?

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I want to look at genera as a whole, across the animal kingdom to determine the range of sizes of genera. I have examined species richness and genetic diversity (pairwise distance from sequence data sets), but I am looking to find more ways to look at 'how big is a genus?' in terms of biodiversity. Any ideas or comments are greatly appreciated!

Bearing in mind that the information is bound to be incomplete (as is the list of existing species), you could use the NCBI taxonomy database. For example, checking the page for the Drosophila genus will give you an idea of its size.

For more precise numbers, you can download thetaxdump.tar.gzfile from NCBI's FTP server (link), extract it and run the script below on the filenodes.dmp(a dump of the database info).

#!/usr/bin/perl use strict; use warnings; use Getopt::Std; my (%opts,%children,%ranks); getopts('t:',\%opts) || do { print STDERR "Invalid option"; exit(1); }; my $taxid=$opts{t}||die "Need a taxid: -t
"; sub getchildren{ my $p=shift; ## The taxid of interest my $found=0; ## will be 0 unless we find a new kid ## For each child of this taxid foreach my $kid (keys%{$children{$p}}){ ## Get the kid's kids foreach my $gkid (keys%{$children{$kid}}){ ## If this one hasn't been seen before unless (defined($children{$p}{$gkid})) { ## Add it to the list of this taxid's children $children{$p}{$gkid}++; ## We found a new one, we need to test again. $found=1; } } } ## If we found a new one, run again getchildren($p) if $found==1; } while (<>) { ## Remove trailing newlines chomp; ## Parse the current line my ($name,$parent,$rank,$rest)=split(/s*|s*/); ## Save the current taxid as a child of its parent $children{$parent}{$name}++; ## Save its rank (species, genus, order etc) $ranks{$name}=$rank; } ## Recursively get all children of this taxid getchildren($taxid); # Count only species as children my @kids=grep($ranks{$_} eq "species", keys(%{$children{$taxid}})); # Print out the results printf "Genus %s has %s members
", $taxid, scalar(@kids);

Assuming you are on or have access to a *nix environment, save that file asgenus.pland run it on thenodes.dmp, giving the taxid of your genus of interest:

perl -t 9257 nodes.dmp

The output of the above example (Ornithorhynchus) is:

$ perl -t 9257 nodes.dmp Genus 9257 has 1 members

If we try on Drosophila, we get:

$ perl -t 7215 nodes.dmp Genus 7215 has 738 members

This is realy not the most efficient way to do it (far better to do this in the script itself but I don't have the time to implement that now), but if you don't mind waiting, this will give you the numbers for all genera:

for i in $(grep -w genus nodes.dmp | awk '{print $1}'); do perl -t $i nodes.dmp; done

Genus sizes are usually measured in number of species, since a particular species under a single taxonomic authority shouldn't be found in more than one genus. Check out Strand and Panova, 2014 for some numbers on number of species found in each genus on average across several thousand genera from eight major taxonomic groups.

What ways are there to determine how big genera are? - Biology

The subcomponents of biological molecules and their sequence determine the properties of that molecule.

Structure and function of polymers are derived from the way their monomers are assembled. In nucleic acids, biological information is encoded in sequences of nucleotide monomers. Each nucleotide has structural components: a five-carbon sugar (deoxyribose or ribose), a phosphate and a nitrogen base (adenine, thymine, guanine, cytosine or uracil). DNA and RNA differ in function and differ slightly in structure, and these structural differences account for the differing functions.In proteins, the specific order of amino acids in a polypeptide (primary structure) interacts with the environment to determine the overall shape of the protein, which also involves secondary tertiary and quaternary structure and, thus, its function. The R group of an amino acid can be categorized by chemical properties (hydrophobic, hydrophilic and ionic), and the interactions of these R groups determine structure and function of that region of the protein. In general, lipids are nonpolar however, phospholipids exhibit structural properties, with polar regions that interact with other polar molecules such as water, and with nonpolar regions where differences in saturation determine the structure and function of lipids. Carbohydrates are composed of sugar monomers whose structures and bonding with each other by dehydration synthesis determine the properties and functions of the molecules. Illustrative examples include: cellulose versus starch.

Directionality influences structure and function of the polymer. Nucleic acids have ends, defined by the 3' and 5' carbons of the sugar in the nucleotide, that determine the direction in which complementary nucleotides are added during DNA synthesis and the direction in which transcription occurs (from 5' to 3'). Proteins have an amino (NH2) end and a carboxyl (COOH) end, and consist of a linear sequence of amino acids connected by the formation of peptide bonds by dehydration synthesis between the amino and carboxyl groups of adjacent monomers. The nature of the bonding between carbohydrate subunits determines their relative orientation in the carbohydrate, which then determines the secondary structure of the carbohydrate.

What ways are there to determine how big genera are? - Biology

Pillbugs are classified as terrestrial isopods and belong to the family of crustacea. This experiment tests the preference of lightness or darkness among pillbugs, commonly referred to as roly-polys. They are slow moving creatures who are cold-blooded: body temperatures are regulated by their environments. Roly-polyprefes r dark, moist environments under rocks, boards, bricks, etc. Pillbugs wander only at night but remain in their habitat throughout the day. Hypothesis: if pillbugs are being experimented on their preference of lightness or darkness then the pillbugs will refer the darkened chamber because their natural habitats involve dark, moist environments.

We came to a conclusion that pillbugs would prefer dark, moist environments under rock, boards,etc. We conducted our experiment with eight pillbugs. Our setup was a choice chamber, we left one side alone while flashing light with a flashlight, while on the other we covered with black construction paper. Then set the pillbugs lose into the choice chamber. Our prediction was wrong, the pillbugs ended up choosing the “light” chamber.

1. Cover choice chamber A with black construction paper.

2. Place a flashlight on top of choice chamber B.

3. Place the 8 pillbugs directly in the center of choice chambers A and B.

4. After 5 minutes of observing and recording switch the construction paper from choice chamber A to choice chamber B and the flashlight from choice chamber B to choice chamber A.

5. Observe the pillbugs over a time period of 5 more minute.

1. Be careful not to point the flashlight directly in the eyes.

2. Always use safety gloves while handling the pillbugs.

2. Be careful not to harm the pillbugs while transferring them to the choice chamber.

Independent Variable: Lighting

Dependent Variable: Number of Pillbugs

Constant: Pillbugs, amount of lighting, amount of darkness

The results show how at the beginning of this experiment the Pill bugs were more attracted to the darker environment but as the time progressed they showed little preference for either side.

According to the Chi Test there is a less than 5% chance that the expected results will occur by chance therefore we will reject our null hypothesis.

Null Hypothesis: Any difference between the observed and expected data is due to chance. If Pill bugs are more attracted to the darker environment then they are also attracted to the light environment.

The results reflect a contradiction with our original hypothesis. We hypothesized that pill bugs would prefer dark environments, however, the data expresses an ambivalence towards the light and dark environments. This is evidenced by very little movement when the environments where switched. However, there was a very thick margin of error. Due to time constraints, only one trial of the experiment was completed. Also, since there was a hand-operated flashlight used instead of a steady lamp, some light could have possibly traveled into the dark choice chamber this could have a detrimental affect on the results. Further research could reveal important aspects of pill bug behavior. Definitive results could be applied to manipulating pill bug environments.

Cited Research

Archer, J. (2004). Sex differences in aggression in real-world settings: A meta-analytic review. Review of General Psychology, 8, 291-322.

Barnett, R. & Rivers, C. (2004). Same difference: How gender myths are hurting our relationships, our children, and our jobs. New York: Basic Books.

Eaton, W. O., & Enns, L. R. (1986). Sex differences in human motor activity level. Psychological Bulletin, 100, 19-28.

Feingold, A. (1994). Gender differences in personality: A meta-analysis. Psychological Bulletin, 116, 429-456.

Halpern, D. F. (2000). Sex Differences in Cognitive Abilities (3rd Edition). Mahwah, NJ: Lawrence Erlbaum, Associates, Inc. Publishers.

Halpern, D. F. (2004). A cognitive-process taxonomy for sex differences in cognitive abilities. Current Directions in Psychological Science, 13 (4), 135-139.

Hyde, J. S., Fennema, E., & Lamon, S. (1990). Gender differences in mathematics performance: A meta-analysis. Psychological Bulletin, 107, 139-155.

Hyde, J. S. (2005). The Gender Similarities Hypothesis. American Psychologist, Vol. 60, No. 6.

Leaper, C. & Smith, T. E. (2004). A meta-analytic review of gender variations in children's language use: Talkativeness, affiliative speech, and assertive speech. Developmental Psychology, 40, 993-1027.

Oliver, M. B. & Hyde, J. S. (1993). Gender differences in sexuality: A meta-analysis. Psychological Bulletin, 114, 29-51.

Spencer, S. J., Steele, C. M. & Quinn, D. M. (1999). Stereotype threat and women's math performance. Journal of Experimental Social Psychology, 35, 4-28.

Voyer, D., Voyer, S., & Bryden, M. P., (1995). Magnitude of sex differences in spatial abilities: A meta-analysis and consideration of critical variables. Psychological Bulletin, 117, 250-270.

Examples of Binomial Nomenclature

Felis concolor

The scientific name Homo sapiens is used to describe the human species. It combines parts of the Latin words hom, meaning human, and sapien, meaning wise. This descriptor of humans tells us many things about the species. First and foremost it defines humans as part of the genus Homo, which includes several extinct species of early humans and modern humans. While we are the only living species in the genus Homo, the specific epithet describes our supposed separation from other species in the genus. Homo neaderthalensis for example, is hypothesized to have gone extinct because of competition from Homo sapiens, or modern humans. Many theorize that it was advanced tool use and language in Homo sapiens that gave them an edge. Modern DNA analysis has shown that Neanderthal genes still exist within the human population, suggesting the two may have interbred at certain points. The binomial nomenclature used here serves to clarify between different forms of organisms through evolutionary time, as well as clarify that all humans are being discussed.

We imagine that children do not belong to the same species as adults -- that they have needs and desires different from ours. But a child's psychology is rather like our own.

We imagine that children do not belong to the same species as adults -- that they have needs and desires different from ours. But a child's psychology is rather like our own.

How big is the average penis?

“I was in the pool!” George Costanza’s distress at the “shrinkage” of his penis after exiting a cold pool was hilarious in the 1994 Seinfeld episode, but for many men concern over the length and girth of their reproductive organ is no laughing matter. Now, a new study could assuage such worries with what may be the most accurate penis-size measurements to date.

Many earlier studies relied on self-reporting, which doesn’t always yield reliable results. “People tend to overestimate themselves,” says David Veale, a psychiatrist at the South London and Maudsley NHS Foundation Trust. So when Veale and his team set out to settle the score on penile proportions, they decided to compile data from clinicians who followed a standardized measuring procedure.

Published today in the British Journal of Urology International, their new study synthesizes data from 17 previous academic papers that included measurements from a total of 15,521 men from around the world. The data enabled the researchers to calculate averages and model the estimated distribution of penile dimensions across humanity. “It still just strikes me how many men have questions and insecurities and concerns about their own penis size. We actually do need good data on it,” says Debra Herbenick, a behavioral scientist at Indiana University, Bloomington, who was not involved in the study.

According to the team’s analysis, the average flaccid, pendulous penis is 9.16 cm (3.61 inches) in length the average erect penis is 13.12 cm (5.16 inches) long. The corresponding girth measurements are 9.31 cm (3.66 inches) for a flaccid penis and 11.66 cm (4.59 inches) for an erect one.

A graph of the size distribution shows that outliers are rare. A 16-cm (6.3-inch) erect penis falls into the 95th percentile: Out of 100 men, only five would have a penis larger than 16 cm. Conversely, an erect penis measuring 10 cm (3.94 inches) falls into the 5th percentile: Only five out of 100 men would have a penis smaller than 10 cm.

Gentlemen, if you’re eager to see how you measure up, you’ll need to follow the same measurement procedure used in the study. All length measurements were made from the pubic bone to the tip of the glans on the top side of the penis. Any fat covering the pubic bone was compressed before measurement, and any additional length provided by foreskin was not counted. Circumference was measured at the base of the penis or around the middle of the shaft, as the two sites were deemed equivalent.

The researchers concluded that there was no strong evidence to link penis size to other physical features such as height, body mass index, or even shoe size. Yes, it seems that the only definite conclusion that can be drawn about a fellow with big socks is that he probably has big feet. Likewise, the study found no significant correlation between genital dimensions and race or ethnicity, although Veale points out that their study was not designed to probe such associations, because much of the data used were from studies of Caucasian men.

It’s easy to laugh at poor George Costanza for his shrunken manhood, but some reports suggest that only about 55% of men are satisfied with their penis size. Some seek potentially dangerous surgical solutions to a problem that, according to Veale, is often only in their head. Men “seem to have a very distorted picture of what [size] other men are, and what they believe they should be,” Veale says.

Pornography, in which male performers are often selected for their extremely large genitalia, may be partly to blame. Similarly, Herbenick points to the myriad spam e-mails that assert that 17.78 cm (7 inches) is average for an erection, when in reality such a member would place its owner in about the 98th percentile. It’s best to just ignore those ads in any case, Veale says. “There are no effective lotions or potions or pills.”

What Is the Scientific Classification of a Monkey?

All monkeys belong to the Kingdom Animalia, the Phylum Chordata, the Class Mammalia and the Order Primates. In the Order Primates, there are two families comprised of monkeys. These are the Cebidae, or New World monkeys, and the Cercopithecidae, or Old World monkeys. There are several genera of monkeys in each of these families and many species within each genus.

Whether a monkey is classified as an Old World or New World species depends on several characteristics. Among these are the quality of the tail, the structure of the nose and the dental arrangement. New World monkeys tend to have prehensile tails or no tail, while Old World monkeys have tails, but they are never prehensile. Old World monkeys have eight, rather then 12 premolars, and their nostrils face downward, while New World monkeys have nostrils that point upwards.

Common species of Cebidae monkeys are the capuchin monkey and golden lion tamarin. Capuchin monkeys fall into several genera. The genus Sapajus includes the large-headed capuchin and the Margarita Island capuchin, among others. The genus Cebus includes the white-fronted and white-faced capuchins. The golden lion tamarin is a member of the genus Leontopithecus, in which there are four separate, yet similar species of lion tamarins. Common Old World monkey genera include Chlorocebus, which includes the Green monkey species, and Macaca, which includes many species of macaques.

What's Next?

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