Download Akemi Corralz Instructor: Professor Schaefer Human Origin 1020

Akemi Corralz
Instructor: Professor Schaefer
Human Origin 1020
January 24, 2014
Lab Report
Darwin’ Finches
Introduction
The Oxford Journal reports the studies on the “Molecular Biology and Evolution” that
was conducted by the group of scientist. The purpose of this research is to identify the
species group that are most closely related to Darwin’s finches, also to identify the grassquit genus Tiaris and Tiaris obscura that will relate to living relative of Darwin’s finches.
Their study showed Darwin’s finches compromise a group of 15 species endemic to
Galapagos 14 species and one species to Coco’s Island. These group of ancestral species
are monophyletic that are known to be migrated to Galapagos Archipelago from Central
or South America, then their descendants have departed and colonized into Coco’s Island.
It was approximately 2.3 million years ago when the ancestors of Darwin’s finches
(Tiaris group) departed for Galapagos Island, Caribbean Island, Central and South
America, during the earth climate was changing dramatically.
There were various birds in Galapagos Island when Darwin observed and studied them
and the plants. Especially, he noticed that many birds shared the similarities with the
ones in the mainland of South America, but they were not identical to the Galapagos. His
collections were 13 finches. He was certain that they were physically different traits.
When he observed, he recognized the different shapes and sizes of their beaks from a
ground finches, tree finches, woodpecker finches and a warble finches. Late, he realized
that Galapagos finches had descendant ancestor that are evolved and adapted the habitats
to the island’s environment.
The scientifical research to identify the species were through sequences of two
mitochondrial (mt) DNA segments (922 bp of the cytochrome b gen and 1,082 bp of the
control region), as well as two nuclea markers (830 bp of numt2, consisting of 140 bp of
mtDNA control region and 690 bp of flanking nuclear DNA). In addition, mtDNA
cytochrome b sequences of some 180 additional Fringillidae species from the database
for phylogeny reconstruction by maximum-parsimony, maximum-likelihood, minimumevolution, and neighbor-joining method were used to identify the grassquit genus Tiaris,
and the species Tiaris obscura as the nearest living relative of Darwin’s finches.
Hypothesis
Through the context of scientifical and biological testing of sequences by the experts, we
are certain to prove the identity of species groups that are most the relative to Darwin’s
finches, including grass quit Tiaris genus and the species Tiaris obscura. In this study we
had an assistant ornithologist, who examined and described from the collected birds skin,
including all the Galapagos finches in the genus Geospiza.
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Materials and Methods
We used birds and their blood samples that are collected from their wing veins. Each
bird was also identified by the local ornithologist and photographed along with
documentation for inspection. There were additional specimen of Tiaris Canora,
Coryphospingus cucullatus, Poospiza hipanoilenis including nine specimens of Tiaris
obsura were sampled. All the blood was collected in an AS-Buffer, blood kit that was
later be used for DNA extraction. We were not able to bet a voucher specimens
procedure that needed their government permission. Also, Polymerase Chain Reaction,
cloning, and sequencing were conducted. When this reaction were proceeded, each clone
was sequenced in both directions at least two independent clones that were sequenced
form each individual. When Phylogenetic reconstruction were under taken, the MP
(maximum-parsimony), ML (maximum-likelihood), and ME (minimum-evolution) and
NJ (neighbor-joining) analyses were preceded with using the PAUP program. It was to
minimize the influence of possible confounding factor in rate variation and compositional
bias. The only PAUP program was used for the MP analyses search methods. There
were branch-swapping using tree bisection and reconnections. Also, PAUP search
method was to construct the ME trees. As we isolated DNA from blood samples using
the long PCR method, amplified it by PCR, either sequenced the amplification product
directly or cloned as sequenced them. Our focus was on four DNA segment, that in some
case the reamplification was necessary. Through the comparison of the sequences, the
identies and sequences have obtained all of the species that were tested. As the four
DNA segments were chosen to sample slowly, the sequences obtained from each DNA
were aligned and examined for evidence of base composition bias, sequence saturation
and rate variation. The main focus of research was on the finches-like bird family of
Fringillidae in which to identify as the tribe of Darwin’s finches. The tribes of birds were
all sampled in the Neotropical region: Thraupini, Emberizini, Parulini, Icterini,
Cardinalini and Carduelini.
Results
Organization of Nuclear Mitochondrial
DNAs
Figure 1.—Organization of nuclear mitochondrial DNAs
(numts) in Darwin's finches and related birds. numt1 is shown
here for comparison; it is restricted to Darwin's finches (see Sato
et al. 1999<$REFLINK> ). mt = mitochondrial; cr = control
region;cytb = cytochrome b.
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Long PCR
Figure 2.—Examples of long PCR used to distinguish genuine
mtDNA sequences from mtDNA fragments integrated into
nuclear DNA (numts). M = size marker (λ phage; indicated
sizes are in kb); Cefu = Certhidea fusca; Tibi = Tiaris bicolor;
Meri = Melanospiza richardsoni; Lono = Loxigilla noctis.
Plots of Transitions
Figure 3.—Plots of transitions (Ts) or
transversions (Tv) in pairwise comparisons at
each site of (A) cytb, (B) cr, (C) numt2, and (D)
numt3 sequences against the corresponding total
percentages of Tv or Ts divergence. The taxa
compared were Darwin's finches (except for the
Cocos finch numt3), Tiaris obscura, Tiaris
canora, Tiaris bicolor, Loxigilla noctalis, and
Melanospiza richardsoni. The x axis shows Ts or
Tv substitutions per site measured as the
uncorrected percentage of sequence divergence.
The ordinate axis shows the mean percentage
(over all pairwise comparisons) of Tv (filled
squares) or Ts (open circles) per site
corresponding to a fixed number of Ts or Tv,
respectively, found in the same pairwise
comparisons
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Cytochrome b Gene Sequences
Figure 4.—Strict consensus of three best
maximum-parsimony trees of the cytb gene
sequences. The tree was made using heuristic
approaches and indicates topological
relationships only. There were 322 parsimonyinformative characters (921 sites in total and no
gaps). Each of the three best trees found had
1,723 steps and differed only in the position of
Loxigilla noctis and Tiaris canora. A number on
a node indicates the percentage recovery of that
node in 500 bootstrap replications; values below
10% are not shown. Analysis of substitutional
saturation indicates that deep divergences may be
misconstructed (the Ts-to-Tv ratio falls from 10:1
within the Darwin's finch [DF] group to close to
1:1 in comparisons to nonthraupine finches).
There is little evidence of substantial saturation
up to and including comparisons between DF and
Tiaris, Loxigilla, and Melanospiza species, in
which transition : transversion ratios are in the
range of 5:1 to 10:1. Plus signs and minus signs
following species names indicate the presence or
absence of numt2 (first symbol) and numt3 (second symbol). In this figure and in the figures that follow,
the sequences are identified by their GenBank accession codes
Maximum-likelihood
Figure 5.—Maximum-likelihood tree
obtained using cytb sequences of those
species found to be most closely related to
the Darwin's finch (DF) group by various
tree-drawing methods applied to the four
DNA sequence data sets. Poospiza
hispaniolensis is included as an outgroup.
The estimated transition : transversion ratio is
4.747 (κ = 9.390), and the α parameter is
0.202. Numbers below nodes show bootstrap
recovery in 500 replications. During
bootstrapping, trees with approximate likelihoods of 5% or farther away from the target score were rejected
without additional iteration. The log likelihood of the tree shown is −3,129.739. The scale bar indicates the
number of substitutions per site
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Strict consensus of two best maximum-parsimony trees
Figure 6.—Strict consensus of two best
maximum-parsimony trees of the control
regions (crs) of selected Darwin's finches
(DF) and their closest relatives. Each of the
two best trees had 404 steps and differed only
in the placement of the Cocos finch within
the Darwin's finch group. Coereba flaveola is
always more distant than the Tiaris group
from the Darwin's finches and is used here to
root the tree. Transversions are weighted five
times transitions for all cr sites. Removal of
the weighting or an alternative selection of Darwin's finch representatives does not alter the topology of the
tree. A number below a node indicates the percentage recovery of that node in 500 bootstrap replications
Maximum-likelihood Reconstruction of Numt3 Phylogeny
Figure 7.—Maximum-likelihood reconstruction of
numt3 phylogeny. The initial tree, branch length,
and rate variations were obtained from a minimumevolution tree. The DNA segment has an estimated
transition : transversion ratio of 2.839 (κ = 5.687)
and a γ shape parameter of 0.563. Numbers below
nodes show bootstrap recovery in 500 replications.
During bootstrapping, trees with approximate
likelihoods of 5% or farther away from the target
score were rejected without additional iteration.
The tree obtained has a log likelihood of
−2,120.820. The scale bar indicates the number of
substitutions per site. DF = Darwin's finches
From the various phylogenetic reconstruction, we found that Darwin’s finches
consistently clustered with five Thraupini species: T. obscura, T. bicolor, T. canora, M.
richardsoni, and L. noctis. They are the five living species that re most closely related to
Darwin’s finches among the other species through our survey. To refer them as the
“Tiaris group.” The statistical support for the geospizini was that Tiaris group clade
came very high, in which was to 100% in terms of bootstrap values. Further support of
clad is consistency of grouping observation in application of the four method of
phylogenetic reconstruction and its recovery in analysis of all four genomic segments by
shared derived substitutions and insertion/deletion in the various segments. The clade
was joined in most of the trees less consistently by Coereba flaveola and volatina
jacarina, which they all proposed candidates on morphological grounds.
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In all cases, it was based on the use of four tree-drawing programs that Tiaris group
turned out as the closest of the Fringillidae clade of the Darwin’s finches which followed
by c. flavela and v. jacarina. According to four method of phylogenetic analysis to the
sequences yielded trees in which the Tiaris species also formed a sister to Darwin’s
finches. The bootsrap support for the geospizine that Tirais group cluster was 99% high
in most of the trees. In all test with no exception that the dull-colored as a sister species
of Darwin’s finches clade. Therefore, T. obscura would be the closest and true relative or
an ancestor of Darwin’s finches among the other species that we surveyed.
Conclusion
There was no fossil record available of Thraupini which could be used to calibrate to
molecule clock of the cytochrome b segment, so Shilds and Wilson were used. This
calibration was based on the fossil record of ungulate mammals assuming a rate of 0.5%
divergence in third-position trans versions per million years. Good case is that both rate
have been widely used in studies of many vertebrae taxa and thraupine birds.
Unfortunately, there is no calibration of erosion rate available in which based on the
control region for geese are unsuited as well as the control of finches.
We are determined that both T. obscura and Darwin’s finches represent the Tiaris
ancestors on the Galapagos Archipelago, even though Darwin’s finding flocks is no
longer exist today. If T. obscura process a blunt beak, then it evolved on Galapagos
warbler-like finch, and lineage secondarily evolved into a blunt-like beak that gave rise to
remaining of extent geospinzine species. Both T. obscura and warbler finches may have
evolved into warbler-like morphology on the mainland. Unfortunately, there is absence
of detailed and well supported phylogeny of the genus Tiaris that currently we are unable
to reconstruct the morphological evolution and distinguish between the possibilities.
Although, we believe in various ecological niches are available on the Archipelago that
triggered a round of adaptive radiation process to this day.
Discussion
The scientific method is half observe and half research on issues. Scientific hypothesis is
testable and falsifiable which is to prove wrong or if it is not proved—it will not be a
scientific hypothesis. It is all through test/collect data/experiment/analyze data. In the
conclusion, either a data will support hypothesis or disprove hypothesis. The various
scientific testing method will conduct and we can only hope for the best theories through
hypothesis. Although, in the end its method is either supportive or disprove hypothesis,
so the scientific method is always retesting and reproving of the issues. Science is so
important and its mission is always exploration for a better future. The use of scientific
method varies in human culture, language, animal, plants and space. There is
paleoanthropology studies that relate to people of early hominins and their remains.
Forensic anthropology deals with legal matter in investigation of crime scenes. Medical
anthropology deal with medicine to cure the disease. Garbology is for practical purpose
in study of garbage that is collected, from food and everything in the trash. This activity
showed the various scientific method that experimented test of collection of samples of
the species. It showed all the data graphs that proved from the field work where
samplings were collected. This research focused through the evolutionary perspective of
the species that have gone through their mutations over times.
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Theory of evolution by natural selection and its underlying assumptions: The natural
biological variation in population is that natural selection operates on individuals. It is
the population that evolves and the unit of evolution is the population that changes and
acquired by its needing. Natural selection of variation is favorable/unfavorable/neutral,
depends on environment change, since evolution is random—never ending of adaption
and readaption. And its response to environmental change. Biological inheritance is an
acquired characteristics and competition of generational survivals. If individual has a
favorable variation is more likely to survive and leave more offspring. He or she will
have reproductive success of sexual selection in favorable variation in frequencies that
become more common in population. Unfortunately, the natural selection for
unfavorable will not be able to compete, defend will have no or less reproduction. They
will have less or no success for being unfavorable ones. The natural selection only works
with variation that already exist and can act only on traits that affect reproduction.
This activity support the theory of evolution that Darwin’s finches have survived through
natural selection over the years. It proved the birds of Tiaris obsucua relate to the living
relatives of Darwin’s finches, having generation of ancestors and their kinds of survived
species. The natural selection of favorable variation is as important as going through the
process in random evolution.
References
Jurmain, Kilgore, and Trevathan, (2013). Human Origins: Evolution and Diversity.
Mason, Ohio: Cengage Learning Custom Solution. Page 27-48.
“On the Origin of Darwin’s Finches,” Molecular Biology and Evolution, Akie Sato,
Herbert Tichy, Colm O’hUigin, Peter R. Grant, B. Rosemary Grant and Jan Klein,
October 24, 2000, accessed on January 20, 2015 at
<http://mbe.oxfordjournals.org/content/18/3/299.full
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