Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
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. 1 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. 2 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 3 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 4 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. 5 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. 6 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 7