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7.3: Gnetophytes - Biology

7.3: Gnetophytes - Biology


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Gnetophytes represent an anatomically and genetically difficult group to classify. However, the true nature of this evolutionary relationship remains murky and contentious.

Characteristics of Gnetophytes

  • Angiosperm-like features: vessel elements, double fertilization, fruit-like ovule coverings
  • Dioecious. Female plants have covered ovules, while male plants have pollen cones.
  • Leaves xerophytic with opposite arrangement
  • Primarily insect pollinated; brightly colored seeds are dispersed by birds

Notable Gnetophytes

Welwitschia mirabilis

This strange plant grows in the desert of Namibia. It has two large leaves that grow from a basal meristem.

Figure (PageIndex{1}): In this small Welwitschia mirabilis, the two large leaves can be seen extending from the central, flat stem. The leaves grow from a basal meristem. The tips of the leaves are ragged, as these are the oldest parts. The leaves are shiny and the setting is dry, indicating their xerophytic nature. In the center, where the two leaves meet, branching stalks terminate in megastrobili. Photo by Waldier CC-BY-NC https://www.inaturalist.org/observations/53253603.

Figure (PageIndex{2}): A larger, older Welwitschia mirabilis. The leaves have split many times and have piled atop themselves. Photo by Alex Dreyer, some rights reserved (CC-BY-NC) https://www.inaturalist.org/observations/10955206.

Figure (PageIndex{3}): Megastrobili of the female Welwitschia mirabilis. These magastrobili are composed of tightly overlapping megasporophylls. Seeds are produced within these structures. Note the short, woody stem at the base of the plant. Photo by juddkirkel, some rights reserved (CC-BY-NC) https://www.inaturalist.org/observations/10852984.

Figure (PageIndex{4}): A closer view of a megastrobilus. Note the opposite arrangement of the megasporophylls. Photo by Christoph Moning, some rights reserved (CC-BY-NC) https://www.inaturalist.org/observations/37703609.

Figure (PageIndex{5}): Male Welwitschia mirabilis plants produce microstrobili. These are smaller, a bit more red-to-pink, and thinner than the megastrobili. Photo by Luis Querido CC-BY-NC https://www.inaturalist.org/observations/8236366.

Figure (PageIndex{6}): Microstrobili of a male Welwitschia mirabilis. These cones are composed of many overlapping microsporophylls. Pollen is produced within microsporangia held on the microsporophylls. Photo by Peter Weston, some rights reserved (CC-BY-NC) https://www.inaturalist.org/observations/10915774.

Ephedra spp.

Figure (PageIndex{7}): A thin stem of Ephedra aspera showing opposite leaf arrangement of two scale-like leaves. Photo by Fred Melgert / Carla Hoegen CC-BY-NC https://www.inaturalist.org/observations/9817627.

Figure (PageIndex{8}): Megastrobili of a female Ephedra distachya. These structures are swollen and red, making them appear fruit-like. Seeds are produced within these structures. Photo by Ramazan_Murtazaliev CC-BY-NC https://www.inaturalist.org/observations/53977932

Figure (PageIndex{9}): Microstrobili of a male Ephedra californica. These small structures look like inflorescenses with anthers emerging. From between the microsporophylls, branching structures emerge, topped with yellow pollen. Photo by Fred Melgert / Carla Hoegen CC-BY-NC https://www.inaturalist.org/observations/21754319.


Biology

Biology is the scientific study of life. [1] [2] [3] It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. [1] [2] [3] For instance, all living organisms are made up of cells that process hereditary information encoded in genes, which can be transmitted to future generations. Another major theme is evolution, which explains the unity and diversity of life. [1] [2] [3] Finally, all living organisms require energy to move, grow, and reproduce, as well as to regulate their own internal environment. [1] [2] [3] [4] [5]

Biologists are able to study life at multiple levels of organization. [1] From the molecular biology of a cell to the anatomy and physiology of plants and animals, and evolution of populations. [1] [6] Hence, there are multiple subdisciplines within biology, each defined by the nature of their research questions and the tools that they use. [7] [8] [9] Like other scientists, biologists use the scientific method to make observations, pose questions, generate hypotheses, and perform experiments to learn about the world around them. [1]

Life on Earth, which emerged more than 3.7 billion years ago, [10] is immensely diverse. Biologists have sought to study and classify the various forms of life, from prokaryotic organisms such as archaea and bacteria to eukaryotic organisms such as protists, fungi, plants, and animals. These various living organisms contribute to the biodiversity of an ecosystem, where they play specialized roles in the cycling of nutrients and energy.


Topic 7.3: Evolution may lead to speciation (AQA A-level Biology)

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Allopatric and sympatric speciation (AQA A-level Biology)

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  • The importance of genetic drift in causing changes in allele frequency
  • Allopatric and sympatric speciation

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Results

Synthesis of comparative and ab initiogene prediction algorithms

The GENSCAN, GeneMark and SNAP prediction tools utilizing ab initio algorithms yielded 32,020, 24,579, and 24,451 A. gambiae CDSs, respectively. The Ensembl database, based on the Genewise comparative algorithm, predicts 16,148 CDSs. To synthesize this set of 97,098 predicted CDSs into a single composite set, we used an exon-gene-union (EGU) algorithm and open-reading-frame-selection algorithm.

First, CDSs predicted by GENSCAN and GeneWise were joined using the EGU algorithm (Figure 1). These two gene model sets were used because GENSCAN was found to be one of the most accurate ab initio gene prediction tools [11, 12], and GeneWise was one of the most accurate comparative prediction methods [12]. The EGU algorithm can be summarized as: Base-pair of CDSs = base-pair predicted by Ensembl ∪ base-pair predicted by GENSCAN. The EGU algorithm involves two program steps: first, consider all the GENSCAN and Ensembl predicted exons as exons of a final CDS and second, if exons from GENSCAN and Ensembl have different boundaries, extend the boundary to include all predicted base-pairs.

Diagram of EGU algorithm. The algorithm considers all exons predicted by GENSCAN and Ensembl as potential exons of a final CDS, and examines exon boundaries to assemble a new gene model. If exons from GENSCAN and Ensembl have different boundaries, the algorithm extends the exon boundary to include all nucleotides of the ab initio and comparative predictions. Subsequently, the ORF-selection algorithm (described in the text) chooses the best translatable reading frame to yield the final ReAnoCDS05 gene model.

Because the newly predicted CDSs from the EGU algorithm do not necessarily have correct open reading frames (ORFs), an ORF-selection algorithm was used to select the best ORF according to the following criteria for ORF-selection implemented in three steps. In step 1, if more than 90% of a new CDS sequence can be translated directly without disruption by a stop codon, keep the transcript as the final CDS. In step 2, if the condition in step 1 is not met, select the predicted CDS from Ensembl, GENSCAN, GeneMark or SNAP that has the first initial exon and the last terminal exon and use this as the predicted CDS. In step 3, if neither steps 1 or 2 apply, select the predicted CDS from Ensembl, GENSCAN, GeneMark or SNAP that has the longest CDS and use this as the predicted CDS. These methods for synthesizing a number of predictions into a single re-annotation err on the side of inclusiveness by retaining the CDS with the greatest genomic extent between initial and terminal exons.

Through these combinatorial algorithms, we generated a total of 31,254 unique CDS predictions. Of these, 25,491 (81.5%) can be translated directly without interruption by internal stop codons, fulfilling step 1 of the ORF-selection algorithm above. About 11.5% (n = 3,583) have at least one ORF predicted from Ensembl, GENSCAN, GeneMark, or SNAP that covers the entire coding region despite possible differences in internal exons, fulfilling step (2) of the ORF-selection algorithm. Finally, the remaining 7% of predicted CDSs (n = 2,180) fulfilled step 3 of the ORF-selection algorithm, where the longest predicted CDS from Ensembl, GENSCAN, GeneMark or SNAP were selected to represent that CDS.

ReAnoCDS05 reannotation dataset

Hereafter we refer to this new set of 31,254 CDSs as ReAnoCDS05 (Table 1). The ReAnoCDS05 dataset is freely available in the Artemis genome viewer [13] format and as FASTA format sequence databases (see Data availabilty in Materials and methods). In ReAnoCDS05, the average number of exons per gene is 4.98, greater than that of Drosophila melanogaster (4.65) and less than that of humans (10.14). Only 4% of predicted CDSs in ReAnoCDS05 lack start and/or stop codons, while in Ensembl 63% of CDSs are incomplete. Of the 31,254 CDSs predicted in ReAnoCDS05, 24,429 were located on chromosomes 2, 3 and X, and another 6,825 CDSs were located on the 'UNKN' virtual chromosome consisting of arbitrarily concatenated unplaced DNA contigs [10]. Some of the CDSs on the UNKN chromosome represent allelic forms of CDSs on known chromosomes [10, 14], and others are probably contamination from bacterial symbionts [15].

Detection of frame shifts in ReAnoCDS05

The 31,254 CDSs in ReAnoCDS05 initially included a small number of frame shifts relative to the original lines of evidence that were merged to generate the final prediction set. The frame shifts largely resulted from annotation errors in the original Ensembl predictions, for example, some introns comprised only one or two nucleotides, presumably to retain reading frame in the Ensembl gene models. The total rate of ReAnoCDS05 genes with frame shifts was about 0.6% (n = 190), which generated protein sequences slightly different from Ensembl or ab initio predictions prior to algorithm synthesis. Because the number of frame-shift cases was very small, however, they were corrected manually.

Evaluation of ReAnoCDS05 by lines of supporting evidence

All CDSs in ReAnoCDS05 were classified based on both empirical and in silico lines of supporting evidence (Figure 2). In addition to those CDSs with Ensembl support (n = 12,720), there are 4,681 novel CDSs with EST support and 3,743 novel CDSs predicted by at least two ab initio algorithms. The latter set of 3,743 CDSs is based upon GENSCAN predictions, and is supported by predictions of one or both of the other ab initio algorithms used. Of predicted ReAnoCDS05 CDSs, 67% (n = 20,970) have more than one line of supporting evidence while 33% (n = 10,284) have only one line of supporting evidence. Of these latter single-evidence predictions, 174 are supported only by Ensembl, and the remaining 10,110 are ab initio predictions supported only by GENSCAN. Of the 10,284 single-evidence CDSs, 28% are assigned to the UNKN chromosome.

Comparison of ReAnoCDS05 and Ensembl CDS sets based on data sources. Total numbers of ReAnoCDS05 CDS predictions in each category related to data sources are indicated within pie slices. Inner ring 12,720, number of ReAnoCDS05 CDSs with Ensembl support inner ring 18,534, ReAnoCDS05 CDSs without Ensembl support. Outer ring slices: 2,414, perfect match between ReAnoCDS05 and Ensembl predictions 6,275, ReAnoCDS05 CDSs that extend and/or merge Ensembl CDSs 4,031, ReAnoCDS05 CDSs that involve major structural changes or reorganization in the overlapping Ensembl CDS(s), where Ensembl CDSs undergo combinations of boundary change, internal exon loss/gain/change, and splitting to >1 ReAnoCDS05 CDS 4,681, novel ReAnoCDS05 CDSs with NCBI dbEST support 3,743, novel ReAnoCDS05 CDSs without EST support but with >1 line of ab initio support 10,110, ReAnoCDS05 CDS with only 1 line of ab initio support.

We subdivided ReAnoCDS05 into two subsets based on lines of supporting evidence: the High-Quality (HQ-CDS) dataset of CDSs with ≥2 lines of support (n = 20,970), and the Low-Quality (LQ-CDS) dataset of CDSs with only one line of support (n = 10,284). The relative biological information content of these prediction sets is functionally evaluated by proteomic assay below.

Validation of ReAnoCDS05 predictions by full-length cDNA dataset

A set of 20,249 full-length cDNA sequences generated as paired contigs [7] were used as a validation test for accuracy of the ReAnoCDS05 reannotation. The 20,249 paired contigs were mapped to 1,885 ReAnoCDS05 CDSs and 2,257 Ensembl CDSs. The number of genes mapped by the paired contigs is smaller than the total number of query sequences because many genes were hit by paired contigs multiple times. Automated comparison of the nucleotide sequences of mapped cDNAs and the ReAnoCDS05 and Ensembl CDSs indicated that 1% of cDNA transcripts placed on the Golden Path sequence were missing from ReAnoCDS05, while 5% were missing from Ensembl, and 45% of ReAnoCDS05 CDSs were annotated completely correctly (exact match of all exon boundaries including start/stop codons), while 30% of Ensembl CDSs met this criterion (Table 1). To extend this analysis, the cDNAs (n = 800) mapped to the X chromosome (n = 156 loci) were used in a detailed manual examination of ReAnoCDS05 and Ensembl CDS support by the cDNA nucleotide sequences and their conceptual translations (Figure 3). Results of the manual analysis were consistent with the automated results, again showing a greater level of precise exon structural and sequence match between cDNAs and ReAnoCDS05 (41%) compared to Ensembl (29%). In this manual analysis, the overall sensitivity of ReAnoCDS05 is 0.99 and of Ensembl 0.92. The manual analysis also indicated that the increased perfect-match level of ReAnoCDS05 was largely due to greater accuracy of start/stop codon prediction by ReAnoCDS05 (28% ReAnoCDS05 and 46% Ensembl disagreement, respectively, with the translated X-chromosome cDNA dataset).

Manual comparison of ReAnoCDS05 and Ensembl based on a set of full-length cDNA sequences. The charts show the analysis of all cDNAs in the dataset mapped to the X-chromosome (n = 800), corresponding to 156 cDNA loci, and their conceptual translation products in relation to CDSs predicted by (a) ReAnoCDS05 and (b) Ensembl. Categories of comparison indicated in the legend are: perfect match, proportion of cDNA sequences with translation products that display exact match to predicted peptide sequence of annotation CDS missing gene, cDNAs not represented by a corresponding annotation CDS exon changes, cDNAs for which the corresponding annotation CDSs display extra exons, missing exons, and/or exon boundary changes different start/stop, cDNA loci for which annotation CDSs display different predicted translation initiation and/or termination merge/split genes, cDNA loci that overlap multiple annotation CDSs, or vice versa other, including multiple low-frequency cases.

The overall specificity of the Ensembl CDS predictions for A. gambiae has not yet been reported. It is difficult to accurately estimate the specificity of either CDS dataset, ReAnoCDS05 or Ensembl, because the A. gambiae genome does not have any exhaustively characterized model regions, analogous to the 30 Mb ENCODE [16] and 2.9 Mb GASP [17] projects in human and Drosophila, respectively, that could serve as a benchmark denominator for determination of specificity. For the purpose of comparison, however, here we assign to the Ensembl CDSs an overall nucleotide specificity of 0.99, which was derived from a test of GeneWise detection of experimental CDSs embedded in semi-artificial genomic sequences [18]. Then, we devised a method to estimate ReAnoCDS05 nucleotide specificity by using the amount of supporting evidence to separate true positive from false positive CDSs, assuming that the majority of single-evidence CDSs in LQ-CDS are false positive (see Materials and methods). The resulting nucleotide specificity for ReAnoCDS05 is calculated to be 0.96, compared to 0.99 for Ensembl (Table 1).

Validation of ReAnoCDS05 predictions by RT-PCR

RT-PCR was used as an additional empirical validation method for a small set of genes to verify ReAnoCDS05 CDSs and evaluate differences with the current Ensembl annotation (Figure 4). RT-PCR assays were designed at sites where ReAnoCDS05 and Ensembl predict different CDS structures, so that the presence and size of product bands unambiguously verify one of the CDS predictions. Maps of the ReAnoCDS05 and Ensembl CDS predictions for the five test categories are shown in Figure 4 (left side of each panel). Five categories of potential difference between ReAnoCDS05 and Ensembl were tested, as follows (corresponding to Figure 4a-e): altered 5' and/or 3' boundaries of ReAnoCDS05 CDSs introduce potential start and/or stop codons not present in Ensembl (Figure 4a) novel ReAnoCDS05 CDSs without Ensembl support (Figure 4b) Ensembl CDSs split into >1 ReAnoCDS05 CDSs (Figure 4c) major structural changes or reorganization in an Ensembl CDSs yields ReAnoCDS05 CDSs with major differences from Ensembl (Figure 4d) >1 Ensembl CDSs merged into 1 ReAnoCDS05 CDS (Figure 4e). Each assay included a positive control reaction with genomic DNA (gDNA) template. A negative control assay in which ReAnoCDS05 and Ensembl both predict no product verified the absence of gDNA contamination in the cDNA template (Figure 4f). In the cases tested, RT-PCR products confirmed the ReAnoCDS05 CDS predictions as compared to the alternative Ensembl predictions. This experimental result complements the validation provided by automated and manual analyses using the larger full-length cDNA dataset above. Although anecdotal rather than quantitative, the RT-PCR analysis at least indicates that these five types of annotation changes actually exist as predicted by ReAnoCDS05.

Validation of ReAnoCDS05 predictions by RT-PCR. Differences between ReAnoCDS05 and Ensembl CDS predictions were experimentally tested by RT-PCR using A. gambiae cDNA or gDNA as templates. The left side of each panel is a map of CDS predictions and supporting lines of evidence, and the right side is a reverse-color image of, from left to right lanes, PhiX/Lambda DNA size standard (Ph), 250 bp DNA ladder (La), and PCR performed on either cDNA (cD), or gDNA template (gD). (a-e) Five cases of potential annotation difference were tested (described in Results) (f) control to test for gDNA contamination of cDNA using primers in two predicted introns to amplify across the intervening exon. In each case except the control, the ReAnoCDS05 and Ensembl annotations made different predictions for the RT-PCR result using cDNA template (in all cases gDNA was the positive control), as follows: (a) ReAnoCDS05 predicted 815 bp, Ensembl predicted no product, RT-PCR estimated 815 bp (b) ReAnoCDS05 predicted 241 bp, Ensembl predicted no product, RT-PCR estimated 241 bp (c) ReAnoCDS05 predicted 1,555 bp, Ensembl predicted no product, RT-PCR estimated 1,555 bp (d) ReAnoCDS05 predicted 1,822 bp, Ensembl predicted no product, RT-PCR estimated 1,822 bp (e) ReAnoCDS05 predicted 1,600 bp, Ensembl predicted no product, RT-PCR estimated 1,600 (f) both ReAnoCDS05 and Ensembl predicted no product, and no product was present. Left panel key: red bars, CDSs from ReAnoCDS05 re-annotation (numbers are ReAnoCDS05 unique IDs) dark green bars, CDSs from Ensembl (with ENSANGT transcript IDs) dark blue bars, CDS from GENSCAN light blue bars, CDSs from GeneMark pink bars, CDSs from SNAP yellow bars, dbEST contigs light green bars, ESTs from immune-enriched cDNA library [45]. All bars on map depict CDSs only, except EST and SNAP, which may also contain UTR sequences. Small gray arrowheads indicate the locations of primers used for verification of CDS structure. Ensembl nucleotide coordinates are shown for the indicated chromosomes.

ReAnoCDS05 improves A. gambiaeproteomic coverage

We generated 8,103 high quality A. gambiae hemolymph peptide sequences by tandem mass spectrometry (MS/MS). Of these peptides, 62% (5,020) do not map to Ensembl proteins, compared to 12% (873) that do not map to ReAnoCDS05. Thus, a dataset of MS/MS peptides was more efficiently populated with cognate protein identities from ReAnoCDS05 than Ensembl, and, therefore, ReAnoCDS05 significantly improved A. gambiae genome annotation coverage.

To determine the basis of the apparently greater information content of ReAnoCDS05 in the MS/MS experiment, we compared the biological information content of the two ReAnoCDS05 CDS subsets (multiple-evidence HQ-CDS and single-evidence LQ-CDS) with Ensembl CDSs using a peptide hit index (PHI see Materials and methods) to determine the MS/MS peptide hit rates in each database. The PHI of the HQ-CDS database (0.305) was greater than that of the Ensembl database (0.190), while the LQ-CDS database displayed the lowest value (0.079). The LQ-CDS dataset should contain a relatively small proportion of correct CDS predictions because the dataset is based on a single line of ab initio support [19]. The low PHI score of the LQ-CDS dataset is consistent with this expectation. Moreover, when PHI scores are normalized to numbers of amino acid residues in each database, the relative rank of each database remained the same (values for (peptide hits/total amino acids in database) × 1,000 are 0.54 for HQ-CDS, 0.45 for Ensembl, and 0.28 for LQ-CDS). This result indicates that the higher PHI score for HQ-CDS is not a consequence of the longer mean CDS length in ReAnoCDS05 compared to Ensembl. This analysis partitions ReAnoCDS05 into high- and low-quality components in terms of biological information content, and indicates that the HQ-CDS CDS dataset specifically enriches the biological information that can be extracted from MS/MS proteomic data as compared to the Ensembl dataset.

ReAnoCDS05 and protein functional annotation

To facilitate data mining and functional annotation of the proteome set, all predicted ReAnoCDS05 proteins were organized in a hyperlinked Excel spreadsheet database, named ReAnoXcel. ReAnoXcel is available for download (see Materials and methods). The ReAnoXcel database contains numerous categories of information for each CDS translation product, including presence or absence of signal peptides indicative of secretion [20], transmembrane domains [21], molecular weight, pI, genome location, and various comparisons to other protein and motif collections, such as the NCBI non-redundant protein database, Gene Ontology [22], CDD [23], and homology to proteins of other organisms, including bacteria, as done before in AnoXcel for the Ensembl proteome set [24].

The ReAnoCDS05 proteome was also compared to the set of 162,565 A. gambiae EST sequences from dbEST (NCBI) and TIGR and assembled into 34,107 contigs and singletons using a combination of the tools BLASTN [25] and the CAP3 assembler [26] as indicated before [27], facilitating verification of the proteome data set. Additionally, the number of sequences from each EST library mapping to unique proteins is indicated. For example, the spreadsheet column named 'Head-all' (including several libraries made from the head of adult mosquitoes) can be sorted to find those proteins with high expression in the adult mosquito head, or the column named 'Blood-fed' (representing approximately 40,000 ESTs of 24 hours post-blood fed mosquitoes) can be compared to the column named 'Non blood-fed' (similar number of ESTs deriving from sugar-fed adult mosquitoes) to find those proteins more expressed after the bloodmeal [28, 29]. A microarray experiment using the Affymetrix whole-genome chip [30] is also mapped to the dataset.

Here we provide only a few possibilities of how ReAnoXcel can be used in data mining. For example, comparison of the reannotated ReAnoCDS05 proteome with the Ensembl set using BLASTP without the low complexity filter identified 1,312 ReAnoCDS05 proteins where the corresponding Ensembl proteins displayed 100% sequence identity but only 50% to 99% of the length of the ReAnoCDS05 proteins. Within these latter 1,312 proteins, apparently truncated in Ensembl, the number of ReAnoCDS05 protein sequences with predicted signal peptides indicative of secretion was 281 in comparison with 211 in the Ensembl set, suggesting that the additional extent of the ReAnoCDS05 proteins is biologically meaningful. Also within the 1,312 set, the average number of membrane helices as predicted by the program TMHMM [21], excluding 0 and 1 helices from both sets, was 5.4 ± 0.29 and 3.7 ± 0.23 (mean ± standard error, n = 214) for ReAnoCDS05 and Ensembl, respectively. In particular, 13 proteins in the ReAnoCDS05 set appeared with 7 transmembrane (7TM) domains, none of which were predicted to be 7TM in the Ensembl set. This is relevant because many proteins containing 7TM domains are membrane receptors [31]. Indeed, the totality of the ReAnoCDS05 set has 159 proteins with predicted 7TM domains, only 86 of which are also predicted as 7TM in the Ensembl set.

Comparison of the proteomes of A. gambiae and D. melanogaster indicated, among other differences, a mosquito expansion of proteases of the trypsin family [32]. These enzymes are involved in protein digestion in the midgut and also in signal transduction and the regulation of proteolytic cascades leading to tissue development and immunity. Digestive trypsins are usually small (approximately 200 to 250 amino acids), while regulatory proteases have additional domains leading to larger proteins. Comparison of the Ensembl proteome set with ReAnoCDS05 shows 318 proteins with the PFAM signature in the Ensembl set, compared with 311 from the ReAnoCDS05 set. In the Ensembl set, 31 proteins overlap with others in their chromosome locations, indicating different predictions of the same gene region, while the ReAnoCDS05 set has 43 such overlapping gene products. Although the two sets have a similar number of predicted trypsins, the Ensembl set has 12 proteins that do not produce identical predictions in ReAnoCDS05, and ReAnoCDS05 produces 65 proteins not predicted in the Ensembl set. Additionally, the average size of the trypsins in the Ensembl set is 298 amino acid residues, while the ReAnoCDS05 set has an average size twice as large, with 687 residues, indicating the possibility that the ReAnoCDS05 set identifies more larger, regulatory trypsins. These comparisons indicate that the ReAnoCDS05 set extends the predictions of the trypsin family in A. gambiae, potentially with better detection of larger regulatory enzymes.

The ReAnoXcel spreadsheet may also facilitate discovery of transposable elements and bacterial transcripts compared to the Ensembl set. Searching for transposons (by searching the strings 'rve,' 'RTV," and 'transposase_' on the CDD results) retrieves 2,896 sequences in the ReAnoCDS05 set as opposed to 132 in the Ensembl database. Also, because the shotgun approach to sequencing the A. gambiae genome used DNA from adult mosquitoes colonized with bacteria, there are many DNA sequences derived from these bacterial symbiont genomes. Recently, whole symbiont genomes were retrieved from shotgun sequencing of Drosophila genomes [15]. To help retrieve these sequences of bacteria associated with A. gambiae, the spreadsheet can be sorted on the best value to NCBI bacterial proteomes, thus yielding 4,655 proteins with BLASTP E-values of 1E-15 or lower. Sorting this subset on the 'chromosome' column retrieves 1,240 sequences on 'UNKN' and further sorting on the taxonomic column facilitates removal of non-bacterial matches to obtain a set of 952 mostly likely bacterial proteins. Resorting of this dataset on the gene 'start' column allows identification of segments of bacterial genomes mapped to the UNKN chromosome, which carries >86% of the high-scoring bacterial homologs.


18.3 Vascular Plants

Vascular plants (from Latin vasculum: duct), also known as tracheophytes (from the equivalent Greek term trachea), form a large group of plants (c. 308,312 accepted known species) that are defined as land plants that have lignified tissues (the xylem) for conducting water and minerals throughout the plant. They also have a specialized non-lignified tissue (the phloem) to conduct products of photosynthesis. Vascular plants include the clubmosses, horsetails, ferns, gymnosperms (including conifers) and angiosperms (flowering plants). Scientific names for the group include Tracheophyta,:251 Tracheobionta and Equisetopsida sensu lato. Some early land plants (the rhyniophytes) had less developed vascular tissue the term eutracheophyte has been used for all other vascular plants.

Botanists define vascular plants by three primary characteristics:

  • Vascular plants have vascular tissues which distribute resources through the plant. Two kinds of vascular tissue occur in plants: xylem and phloem. Phloem and xylem are closely associated with one another and are typically located immediately adjacent to each other in the plant. The combination of one xylem and one phloem strand adjacent to each other is known as a vascular bundle. The evolution of vascular tissue in plants allowed them to evolve to larger sizes than non-vascular plants, which lack these specialized conducting tissues and are thereby restricted to relatively small sizes.
  • In vascular plants, the principal generation phase is the sporophyte, which produces spores and is diploid (having two sets of chromosomes per cell). (By contrast, the principal generation phase in non-vascular plants is the gametophyte, which produces gametes and is haploid - with one set of chromosomes per cell.)
  • Vascular plants have true roots, leaves, and stems, even if some groups have secondarily lost one or more of these traits.

Cavalier-Smith (1998) treated the Tracheophyta as a phylum or botanical division encompassing two of these characteristics defined by the Latin phrase “facies diploida xylem et phloem instructa” (diploid phase with xylem and phloem).:251

One possible mechanism for the presumed evolution from emphasis on haploid generation to emphasis on diploid generation is the greater efficiency in spore dispersal with more complex diploid structures. Elaboration of the spore stalk enabled the production of more spores and the development of the ability to release them higher and to broadcast them farther. Such developments may include more photosynthetic area for the spore-bearing structure, the ability to grow independent roots, woody structure for support, and more branching.

Water and nutrients in the form of inorganic solutes are drawn up from the soil by the roots and transported throughout the plant by the xylem. Organic compounds such as sucrose produced by photosynthesis in leaves are distributed by the phloem sieve tube elements.

The xylem consists of vessels in flowering plants and tracheids in other vascular plants, which are dead hard-walled hollow cells arranged to form files of tubes that function in water transport. A tracheid cell wall usually contains the polymer lignin. The phloem, however, consists of living cells called sieve-tube members. Between the sieve-tube members are sieve plates, which have pores to allow molecules to pass through. Sieve-tube members lack such organs as nuclei or ribosomes, but cells next to them, the companion cells, function to keep the sieve-tube members alive.

The most abundant compound in all plants, as in all cellular organisms, is water, which serves an important structural role and a vital role in plant metabolism. Transpiration is the main process of water movement within plant tissues. Water is constantly transpired from the plant through its stomata to the atmosphere and replaced by soil water taken up by the roots. The movement of water out of the leaf stomata creates a transpiration pull or tension in the water column in the xylem vessels or tracheids. The pull is the result of water surface tension within the cell walls of the mesophyll cells, from the surfaces of which evaporation takes place when the stomata are open. Hydrogen bonds exist between water molecules, causing them to line up as the molecules at the top of the plant evaporate, each pulls the next one up to replace it, which in turn pulls on the next one in line. The draw of water upwards may be entirely passive and can be assisted by the movement of water into the roots via osmosis. Consequently, transpiration requires very little energy to be used by the plant. Transpiration assists the plant in absorbing nutrients from the soil as soluble salts.

Living root cells passively absorb water in the absence of transpiration pull via osmosis creating root pressure. It is possible for there to be no evapotranspiration and therefore no pull of water towards the shoots and leaves. This is usually due to high temperatures, high humidity, darkness or drought.

Xylem and phloem tissues are involved in the conduction processes within plants. Sugars are conducted throughout the plant in the phloem, water and other nutrients through the xylem. Conduction occurs from a source to a sink for each separate nutrient. Sugars are produced in the leaves (a source) by photosynthesis and transported to the growing shoots and roots (sinks) for use in growth, cellular respiration or storage. Minerals are absorbed in the roots (a source) and transported to the shoots to allow cell division and growth.

18.3.1 Ferns

A fern (Polypodiopsida or Polypodiophyta) is a member of a group of vascular plants (plants with xylem and phloem) that reproduce via spores and have neither seeds nor flowers. They differ from mosses by being vascular, i.e., having specialized tissues that conduct water and nutrients and in having life cycles in which the sporophyte is the dominant phase. Ferns have complex leaves called megaphylls, that are more complex than the microphylls of clubmosses. Most ferns are leptosporangiate ferns. They produce coiled fiddleheads that uncoil and expand into fronds. The group includes about 10,560 known extant species. Ferns are defined here in the broad sense, being all of the Polypodiopsida, comprising both the leptosporangiate (Polypodiidae) and eusporangiate ferns, the latter group including horsetails or scouring rushes, whisk ferns, marattioid ferns, and ophioglossoid ferns.

Ferns first appear in the fossil record about 360 million years ago in the middle Devonian period, but many of the current families and species did not appear until roughly 145 million years ago in the early Cretaceous, after flowering plants came to dominate many environments. The fern Osmunda claytoniana is a paramount example of evolutionary stasis paleontological evidence indicates it has remained unchanged, even at the level of fossilized nuclei and chromosomes, for at least 180 million years.

Ferns are not of major economic importance, but some are used for food, medicine, as biofertilizer, as ornamental plants and for remediating contaminated soil. They have been the subject of research for their ability to remove some chemical pollutants from the atmosphere. Some fern species, such as bracken (Pteridium aquilinum) and water fern (Azolla filiculoides) are significant weeds worldwide. Some fern genera, such as Azolla, can fix nitrogen and make a significant input to the nitrogen nutrition of rice paddies. They also play certain roles in folklore.

Like the sporophytes of seed plants, those of ferns consist of stems, leaves and roots. Ferns differ from seed plants in reproducing by spores and from bryophytes in that, like seed plants, they are Polysporangiophytes, their sporophytes branching and producing many sporangia. Unlike bryophytes, fern sporophytes are free-living and only briefly dependent on the maternal gametophyte.

Stems: Fern stems are often referred to as rhizomes, even though they grow underground only in some of the species. Epiphytic species and many of the terrestrial ones have above-ground creeping stolons (e.g., Polypodiaceae), and many groups have above-ground erect semi-woody trunks (e.g., Cyatheaceae). These can reach up to 20 meters (66 ft) tall in a few species (e.g., Cyathea brownii on Norfolk Island and Cyathea medullaris in New Zealand).

Leaf: The green, photosynthetic part of the plant is technically a megaphyll and in ferns, it is often referred to as a frond. New leaves typically expand by the unrolling of a tight spiral called a crozier or fiddlehead into fronds. This uncurling of the leaf is termed circinate vernation. Leaves are divided into two types a trophophyll and a sporophyll. A trophophyll frond is a vegetative leaf analogous to the typical green leaves of seed plants that does not produce spores, instead only producing sugars by photosynthesis. A sporophyll frond is a fertile leaf that produces spores borne in sporangia that are usually clustered to form sori. In most ferns, fertile leaves are morphologically very similar to the sterile ones, and they photosynthesize in the same way. In some groups, the fertile leaves are much narrower than the sterile leaves, and may even have no green tissue at all (e.g., Blechnaceae, Lomariopsidaceae). The anatomy of fern leaves can either be simple or highly divided. In tree ferns, the main stalk that connects the leaf to the stem (known as the stipe), often has multiple leaflets. The leafy structures that grow from the stipe are known as pinnae and are often again divided into smaller pinnules.

Roots: The underground non-photosynthetic structures that take up water and nutrients from soil. They are always fibrous and structurally are very similar to the roots of seed plants.

Like all other vascular plants, the diploid sporophyte is the dominant phase or generation in the life cycle. The gametophytes of ferns, however, are very different from those of seed plants. They are free-living and resemble liverworts, whereas those of seed plants develop within the spore wall and are dependent on the parent sporophyte for their nutrition. A fern gametophyte typically consists of:

Prothallus: A green, photosynthetic structure that is one cell thick, usually heart or kidney shaped, 3–10 mm long and 2–8 mm broad. The prothallus produces gametes by means of: Antheridia: Small spherical structures that produce flagellate sperm. Archegonia: A flask-shaped structure that produces a single egg at the bottom, reached by the sperm by swimming down the neck. Rhizoids: root-like structures (not true roots) that consist of single greatly elongated cells, that absorb water and mineral salts over the whole structure. Rhizoids anchor the prothallus to the soil.

Ferns are widespread in their distribution, with the greatest abundance in the tropics, and least in arctic areas. The greatest diversity occurs in tropical rainforests. New Zealand, for which the fern is a symbol, has about 230 species, distributed throughout the country.

The stereotypical image of ferns growing in moist shady woodland nooks is far from a complete picture of the habitats where ferns can be found growing. Fern species live in a wide variety of habitats, from remote mountain elevations, to dry desert rock faces, to bodies of water or in open fields. Ferns in general may be thought of as largely being specialists in marginal habitats, often succeeding in places where various environmental factors limit the success of flowering plants. Some ferns are among the world’s most serious weed species, including the bracken fern growing in the Scottish highlands, or the mosquito fern (Azolla) growing in tropical lakes, both species forming large aggressively spreading colonies. There are four particular types of habitats that ferns are found in: moist, shady forests crevices in rock faces, especially when sheltered from the full sun acid wetlands including bogs and swamps and tropical trees, where many species are epiphytes (something like a quarter to a third of all fern species).

Especially the epiphytic ferns have turned out to be hosts of a huge diversity of invertebrates. It is assumed that bird’s-nest ferns alone contain up to half the invertebrate biomass within a hectare of rainforest canopy.

Many ferns depend on associations with mycorrhizal fungi. Many ferns grow only within specific pH ranges for instance, the climbing fern (Lygodium palmatum) of eastern North America will grow only in moist, intensely acid soils, while the bulblet bladder fern (Cystopteris bulbifera), with an overlapping range, is found only on limestone.

The spores are rich in lipids, protein and calories, so some vertebrates eat these. The European woodmouse (Apodemus sylvaticus) has been found to eat the spores of Culcita macrocarpa and the bullfinch (Pyrrhula murina) and the New Zealand lesser short-tailed bat (Mystacina tuberculata) also eat fern spores.


Frontiers

Despite considerable progress in our characterization of members of the semaphorin family, much remains to be learned about their functions and molecular mechanisms of action. Several semaphorins have yet to be functionally characterized, and many have undergone only a cursory examination. A number of questions remain, including the purpose of having so many related semaphorins and the underlying logic to their complex expression patterns and physiological roles. The degree of interaction among semaphorins is also poorly understood. Do they regulate each other's signaling cascades? Do they physically associate? What special attributes and abilities do the secreted, transmembrane, and GPI-linked forms of semaphorins functionally provide?

Understanding the signaling cascades that underlie the different functional effects of semaphorins will provide insights into these important proteins. Are there differences in the signaling cascades activated by the different semaphorins? How much do their signaling cascades vary in order to mediate their different cellular effects? How do semaphorins exert their dramatic effects on the cytoskeleton?

A more detailed understanding of the role of semaphorins in the normal functioning adult is important. In the nervous system, the role of semaphorins in forming neural connections is well established, but the role of semaphorins in neural connectivity as it pertains to thought, emotion, memory, and behavior is unknown. The role of semaphorins in human disease and pathology is also poorly understood. Mutations in semaphorins are associated with patients with cancer [28], retinal degeneration [51], decreased bone mineral density [52], rheumatoid arthritis [53], and CHARGE syndrome (a disorder characterized by cranial nerve dysfunction, cardiac anomalies, and growth retardation) [54]. Further characterization of the semaphorins and a better understanding of their signaling mechanisms will undoubtedly uncover additional roles for semaphorins and semaphorin signaling in human disease.

Given the role of semaphorins in a wide range of tissues and functions including neurobiology, vasculobiology, cancer biology, and immunobiology, further characterizing the semaphorins and their signaling cascades will reveal fundamental mechanisms of how these systems work and strategies for preventing and treating pathologies associated with them.


Exam 4 Study Set

2. Began oxygen production about ____ billion years ago.

3. More or less of them than eukaryotes? Bigger or smaller?

2.) Everywhere! Wherever there is life. Deep within the Earth and anywhere that isn't fit for eukaryotes to survive.

3.) Far outnumber eukaryotes. Typically smaller.

4.) about 1/2 of all human diseases can also be beneficial.

2. Evolved from ________ ancestors.

2. More than any other group, protists vary in _________ and ________.

3. Not one distinct group but instead represent ______________ that are not ____,_____, or ______.

3.) all the eukaryotes plants, animals, fungi

Include diatoms and dinoflagellates

2. Include ____ and ____ crops, grains, grasses, and most _____.

2. Sperm of ferns, like those of mosses, have _____ and must ________________ to fertilize eggs.

3. What stage you see most of the time--the fern fronds

4. The haploid stage is _____ (size) and usually ______ (where).

2.) Flagella swim through a film of water

4.) smaller, about the size of a nickel just underground

2. The descendants of early gymnosperms include the ____, or _______ plants, and a few others.

3. All 900+ species are ______ ______ that produce ovules on the edge of a cone-like structure.

2. Include the ____, _____, and _____ organisms on Earth.

Include pines, firs, spruces, redwoods, cedars, cypress, sequoias, larches, tamaracks.

2. Diversified ______ to become the ______ plants in the modern world---__x of the others all combined.

3. Represented by about ______ species.

4. Supply nearly all of our _____ and much of our _____ for textiles.

2. Tremendously ______ and economically important.

3. _____ of enormous importance.

4. What makes this group so successful?

Actually a short stem with 4 whorls of modified leaves-->what are they?

Sepals, Petals, Stamens, Carpels (not all flowers have all parts)

2. ______ organized and lack ______

3. ______ with several types of cells

5. ______ species, mostly marine

7. Adults ____, larvae ______

8. _________ cells draw water through the walls of the sponge where food is collected

2. Soft body with, in many species, protective _____ _____.

4. Unique tongue-like organ

5. Separate sexes although some _______.

7. ________ species living on land, in freshwater, and in oceans.

9. Clams, scallops, oysters, and mussels are.

3.) foot, visceral mass, mantle

Roughly ______ species of bivalve--> most live in ____

2. Tentacles for ____, ____, and _____.

3. Giant squid can grow to ___ feet.

4. Octopus can get up to ___ feet across.

2.) feeding, locomotion, defense

2. The simplest ______ animals.

2. ______ symmetrical with a head.

2. ______ in shape, ______ at both ends.

3. In nearly ____ habitats from poles to tropics.

5. ______ but not circular muscles.

2. A subdivision of the body along its length into a series of repeated parts?

2. Are named for their _____ _____.

3. There are about ____ million of these species identified, mostly insects.

4. Are a very _____ and _____ group, occurring in nearly all habitats in the biosphere.


7.3 Circulatory system NEW Year 12 Biology specification

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This PowerPoint created for the NEW AQA Biology specification includes information slides and pupil activities to achieve the following learning objectives:

1) Explain why large organisms move substances around their bodies and describe the features of their transport systems (C grade)
2) Explain the circulatory systems of insects, fish and mammals (B grade)
3) Explain the relative efficiency of different circulatory systems (A grade)

All activities and the answers are included and fully integrated into the PowerPoint.

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Mass Transport - Haemoglobin, oxygen transport, circulatory systems, structure of the heart, cardiac cycle

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Contents

The first Argentinosaurus bone, which is now thought to be a fibula (calf bone), was discovered in 1987 by Guillermo Heredia on his farm "Las Overas" about 8 km (5 mi) east of Plaza Huincul, in Neuquén Province, Argentina. Heredia, initially believing he had discovered petrified logs, informed the local museum, the Museo Carmen Funes, whose staff members excavated the bone and stored it in the museum's exhibition room. In early 1989, the Argentine palaeontologist José F. Bonaparte initiated a larger excavation of the site involving palaeontologists of the Museo Argentino de Ciencias Naturales, yielding a number of additional elements from the same individual. The individual, which later became the holotype of Argentinosaurus huinculensis, is catalogued under the specimen number MCF-PVPH 1. [1]

Separating fossils from the very hard rock in which the bones were encased required the use of pneumatic hammers. [2] [3] [4] : 35 The additional material recovered included seven dorsal vertebrae (vertebrae of the back), [1] the underside of the sacrum (fused vertebrae between the dorsal and tail vertebrae) including the first to fifth and some sacral ribs, and a part of a dorsal rib (rib from the flank). [2] These finds were also incorporated into the collection of the Museo Carmen Funes. [2]

Bonaparte presented the new find in 1989 at a scientific conference in San Juan. The formal description was published in 1993 by Bonaparte and the Argentine palaeontologist Rodolfo Coria, with the naming of a new genus and species, Argentinosaurus huinculensis. The generic name means "Argentine lizard", while the specific name refers to the town Plaza Huincul. [2] Bonaparte and Coria described the limb bone discovered in 1987 as an eroded tibia (shin bone), although the Uruguayan palaeontologist Gerardo Mazzetta and colleagues reidentified this bone as a left fibula in 2004. [5] [6] In 1996, Bonaparte referred (assigned) a complete femur (thigh bone) from the same locality to the genus, which was put on exhibit at the Museo Carmen Funes. This bone was deformed by front-to-back crushing during fossilization. In their 2004 study, Mazzetta and colleagues mentioned an additional femur that is housed in the La Plata Museum under the specimen number MLP-DP 46-VIII-21-3. Though not as strongly deformed as the complete femur, it preserves only the shaft and lacks its upper and lower ends. Both specimens belonged to individuals equivalent in size to the holotype individual. [5] As of 2019, however, it was still uncertain whether any of these femora belonged to Argentinosaurus. [7]

Size Edit

Argentinosaurus is among the largest known land animals, although its exact size is difficult to estimate because of the incompleteness of its remains. [8] To counter this problem, palaeontologists can compare the known material with that of smaller related sauropods known from more complete remains. The more complete taxon can then be scaled up to match the dimensions of Argentinosaurus. Mass can be estimated from known relationships between certain bone measurements and body mass, or through determining the volume of models. [9]

A reconstruction of Argentinosaurus created by Gregory Paul in 1994 yielded a length estimate of 30–35 metres (98–115 ft). [10] Later that year, estimates by Bonaparte and Coria suggesting a hind limb length of 4.5 metres (15 ft), a trunk length (hip to shoulder) of 7 metres (23 ft), and an overall body length of 30 metres (98 ft) were published. [11] In 2006, Kenneth Carpenter reconstructed Argentinosaurus using the more complete Saltasaurus as a guide and estimated a length of 30 metres (98 ft). [12] In 2008, Jorge Calvo and colleagues used the proportions of Futalognkosaurus to estimate the length of Argentinosaurus at less than 33 metres (108 ft). [13] Holtz gave a higher length estimate of 36.6 metres (120 ft) in 2012. [14] In 2013, William Sellers and colleagues arrived at a length estimate of 39.7 metres (130 ft) and a shoulder height of 7.3 metres (24 ft) by measuring the skeletal mount in Museo Carmen Funes. [15] During the same year, Scott Hartman suggested that because Argentinosaurus was then thought to be a basal titanosaur, it would have a shorter tail and narrower chest than Puertasaurus, which he estimated to be about 27 metres (89 ft) long, indicating Argentinosaurus was slightly smaller. [16] In 2016, Paul estimated the length of Argentinosaurus at 30 m (98 ft). [17] Paul estimated a greater length of 35 metres (115 ft) or longer in 2019, restoring the unknown neck and tail of Argentinosaurus after those of other large South American titanosaurs. [7]

Paul estimated a body mass of 80–100 tonnes (88–110 short tons) for Argentinosaurus in 1994. [10] In 2004, Mazzetta and colleagues provided a range of 60–88 tonnes (66–97 short tons) and considered 73 tonnes (80 short tons) to be the most likely mass, making it the heaviest sauropod known from good material. [5] Holtz estimated a mass of 73–91 tonnes (80–100 short tons) in 2007. [18] In 2013, Sellers and colleagues estimated a mass of 83.2 tonnes (91.7 short tons) by calculating the volume of the aforementioned Museo Carmen Funes skeleton. [15] In 2014, Roger Benson and colleagues estimated the mass of Argentinosaurus at 90 tonnes (99 short tons). [19] In 2016, using equations that estimate body mass based on the circumference of the humerus and femur of quadrupedal animals, Bernardo Gonzáles Riga and colleagues estimated a mass of 96.4 tonnes (106.3 short tons). [20] Paul listed Argentinosaurus at 50 tonnes (55 short tons) or more in the same year. [17] In 2017, José Carballido and colleagues estimated its mass at over 60 tonnes (66 short tons). [8] In 2019, Paul gave a mass estimate of 65–75 tonnes (72–83 short tons) based on his skeletal reconstructions (diagrams illustrating the bones and shape of an animal) of Argentinosaurus in dorsal and lateral view. [7]

While Argentinosaurus was definitely a massive animal, there is disagreement over whether it was the largest known titanosaur. Puertasaurus, Futalognkosaurus, Dreadnoughtus, Paralititan, "Antarctosaurus" giganteus, and Alamosaurus have all been considered to be comparable in size with Argentinosaurus by some studies, [21] [22] although others have found them to be notably smaller. [13] [23] [7] In 2017, Carballido and colleagues considered Argentinosaurus to be smaller than Patagotitan, since the latter had a greater area enclosed by the , , and of its anterior dorsal vertebrae. [8] However, Paul found Patagotitan to be smaller than Argentinosaurus in 2019, due to the latter's dorsal column being considerably longer. Even if Argentinosaurus was the largest-known titanosaur, other sauropods including Maraapunisaurus and a giant mamenchisaurid, may have been larger, although these are only known from very scant remains. Some diplodocids, such as Supersaurus and Diplodocus [24] [7] may have exceeded Argentinosaurus in length despite being considerably less massive. [12] [25] The mass of the blue whale, however, which can be greater than 100 tonnes (110 short tons), [26] still exceeds that of all known sauropods. [7]

Vertebrae Edit

Argentinosaurus likely possessed 10 dorsal vertebrae, like other titanosaurs. [7] The vertebrae were enormous even for sauropods one dorsal vertebra has a reconstructed height of 159 centimetres (63 in) and a width of 129 centimetres (51 in), and the are up to 57 centimetres (22 in) in width. [2] In 2019, Paul estimated the total length of the dorsal vertebral column at 447 centimetres (176 in) and the width of the pelvis at 0.6 times the combined length of the dorsal and sacral vertebral column. [7] The dorsals were (concave at the rear) as in other macronarian sauropods. [2] [6] : 205 The (excavations on the sides of the centra) were proportionally small and positioned in the front half of the centrum. [27] : 102 The vertebrae were internally lightened by a complex pattern of numerous air-filled chambers. Such camellate bone is, among sauropods, especially pronounced in the largest and longest-necked species. [28] [29] In both the dorsal and sacral vertebrae, very large cavities measuring 4 to 6 centimetres (1.6 to 2.4 in) were present. [28] The dorsal ribs were tubular and cylindrical in shape, in contrast with other titanosaurs. [2] [30] : 309 Bonaparte and Coria, in their 1993 description, noted the ribs were hollow, unlike those of many other sauropods, but later authors argued this hollowing could also have been due to erosion after the death of the individual. [6] Argentinosaurus, like many titanosaurs, [31] probably had six sacral vertebrae (those in the hip region), although the last one is not preserved. The centra of the second to fifth sacral vertebrae were much reduced in size and considerably smaller than the centrum of the first sacral. The sacral ribs curved downwards. The second sacral rib was larger than the other preserved sacral ribs, though the size of the first is unknown due to its incompleteness. [2]

Because of their incomplete preservation, the original position of the known dorsal vertebrae within the vertebral column is disputed. Dissenting configurations were suggested by Bonaparte and Coria in 1993 Fernando Novas and Martín Ezcurra in 2006 and Leonardo Salgado and Jaime Powell in 2010. One vertebra was interpreted by these studies as the first, fifth or third and another vertebra as the second, tenth or eleventh, or ninth, respectively. A reasonably complete vertebra was found to be the third by the 1993 and 2006 studies, but the fourth by the 2010 study. Another vertebra was interpreted by the three studies as being part of the rear section of the dorsal vertebral column, as the fourth, or as the fifth, respectively. In 1993, two articulated (still connected) vertebrae were thought to be of the rear part of the dorsal column but are interpreted as the sixth and seventh vertebrae in the two later studies. The 2010 study mentioned another vertebra that was not mentioned by the 1993 and 2006 studies it was presumed to belong to the rear part of the dorsal column. [2] [32] [1]

Another contentious issue is the presence of hyposphene-hypantrum articulations, accessory joints between vertebrae that were located below the main articular processes. Difficulties in interpretation arise from the fragmentary preservation of the vertebral column these joints are hidden from view in the two connected vertebrae. [28] In 1993, Bonaparte and Coria said the hyposphene-hypantrum articulations were enlarged, as in the related Epachthosaurus, and had additional articular surfaces that extended downwards. [2] This was confirmed by some later authors Novas noted the hypantrum (a bony extension below the articular processes of the front face of a vertebra) extended sidewards and downwards, forming a much-broadened surface that connected with the equally enlarged hyposphene at the back face of the following vertebra. [28] [30] : 309–310 In 1996, Bonaparte stated these features would have made the spine more rigid and were possibly an adaptation to the giant size of the animal. [27] Other authors argued most titanosaur genera lacked hyposphene-hypantrum articulations and that the articular structures seen in Epachthosaurus and Argentinosaurus are thickened vertebral (ridges). [28] [33] [34] : 55 Sebastián Apesteguía, in 2005, argued the structures seen in Argentinosaurus, which he termed hyposphenal bars, are indeed thickened laminae that could have been derived from the original hyposphene and had the same function. [35]

Limbs Edit

The complete femur that was assigned to Argentinosaurus is 2.5 metres (8.2 ft) long. The femoral shaft has a circumference of about 1.18 metres (3.9 ft) at its narrowest part. Mazzetta and colleagues used regression equations to estimate its original length at 2.557 metres (8.39 ft), which is similar to the length of the other femur, and later in 2019 Paul gave a similar estimate of 2.575 metres (8.45 ft). [7] By comparison, the complete femora preserved in the other giant titanosaurs Antarctosaurus giganteus and Patagotitan mayorum measure 2.35 metres (7.7 ft) and 2.38 metres (7.8 ft), respectively. [5] [8] While the holotype specimen does not preserve a femur, it preserves a slender fibula (originally interpreted as a tibia) that is 1.55 metres (5.1 ft) in length. When it was identified as a tibia, it was thought to have a comparatively short , a prominent extension at the upper front that anchored muscles for stretching the leg. However, as stated by Mazzetta and colleagues, this bone lacks both the proportions and anatomical details of a tibia, while being similar in shape to other sauropod fibulae. [2] [5]

Relationships within Titanosauria are amongst the least understood of all groups of dinosaurs. [36] Traditionally, the majority of sauropod fossils from the Cretaceous had been referred to a single family, the Titanosauridae, which has been in use since 1893. [37] In their 1993 first description of Argentinosaurus, Bonaparte and Coria noted it differed from typical titanosaurids in having hyposphene-hypantrum articulations. As these articulations were also present in the titanosaurids Andesaurus and Epachthosaurus, Bonaparte and Coria proposed a separate family for the three genera, the Andesauridae. Both families were united into a new, higher group called Titanosauria. [2]

In 1997, Salgado and colleagues found Argentinosaurus to belong to Titanosauridae in an unnamed clade with Opisthocoelicaudia and an indeterminate titanosaur. [38] In 2002, Davide Pisani and colleagues recovered Argentinosaurus as a member of Titanosauria, and again found it to be in a clade with Opisthocoelicaudia and an unnamed taxon, in addition to Lirainosaurus. [39] A 2003 study by Jeffrey Wilson and Paul Upchurch found both Titanosauridae and Andesauridae to be invalid the Titanosauridae because it was based on the dubious genus Titanosaurus and the Andesauridae because it was defined on plesiomorphies (primitive features) rather than on synapomorphies (newly evolved features that distinguish the group from related groups). [37] A 2011 study by Philip Mannion and Calvo found Andesauridae to be paraphyletic (excluding some of the group's descendants) and likewise recommended its disuse. [40]

In 2004, Upchurch and colleagues introduced a new group called Lithostrotia that included the more derived (evolved) members of Titanosauria. Argentinosaurus was classified outside this group and thus as a more basal ("primitive") titanosaurian. [30] : 278 The basal position within Titanosauria was confirmed by a number of subsequent studies. [36] [28] [41] [42] [43] In 2007, Calvo and colleagues named Futalognkosaurus they found it to form a clade with Mendozasaurus and named it Lognkosauria. [44] A 2017 study by Carballido and colleagues recovered Argentinosaurus as a member of Lognkosauria and the sister taxon of Patagotitan. [8] In 2018, González Riga and colleagues also found it to belong in Lognkosauria, which in turn was found to belong to Lithostrotia. [45]

Another 2018 study by Hesham Sallam and colleagues found two different phylogenetic positions for Argentinosaurus based on two data sets. They did not recover it as a lognkosaurian but as either a basal titanosaur or a sister taxon of the more derived Epachthosaurus. [46] In 2019, Julian Silva Junior and colleagues found Argentinosaurus to belong to Lognkosauria once again they recovered Lognkosauria and Rinconsauria (another group generally included in Titanosauria) to be outside Titanosauria. [47] Another 2019 study by González Riga and colleagues also found Argentinosaurus to belong to Lognkosauria they found this group to form a larger clade with Rinconsauria within Titanosauria, which they named Colossosauria. [48]

Topology according to Carballido and colleagues, 2017. [8]

Argentinosaurus

Topology according to González Riga and colleagues, 2019. [48]

Argentinosaurus

The giant size of Argentinosaurus and other sauropods was likely made possible by a combination of factors these include fast and energy-efficient feeding allowed for by the long neck and lack of mastication, fast growth and fast population recovery due to their many small offspring. Advantages of giant sizes would likely have included the ability to keep food inside the digestive tract for lengthy periods to extract a maximum of energy, and increased protection against predators. [49] Sauropods were oviparous (egg-laying). In 2016, Mark Hallett and Matthew Wedel stated that the eggs of Argentinosaurus were probably only 1 litre (0.26 US gal) in volume, and that a hatched Argentinosaurus was no longer than 1 metre (3.3 ft) and not heavier than 5 kilograms (11 lb). The largest sauropods increased their size by five orders of magnitude after hatching, more than in any other amniote animals. [50] : 186 Hallett and Wedel argued size increases in the evolution of sauropods were commonly followed by size increases of their predators, theropod dinosaurs. Argentinosaurus might have been preyed on by Mapusaurus, which is among the largest theropods known. Mapusaurus is known from at least seven individuals found together, [51] raising the possibility that this theropod hunted in packs to bring down large prey including Argentinosaurus. [50] : 206–207

In 2013, Sellers and colleagues used a computer model of the skeleton and muscles of Argentinosaurus to study its speed and gait. Before computer simulations, the only way of estimating speeds of dinosaurs was through studying anatomy and trackways. The computer model was based on a laser scan of a mounted skeletal reconstruction on display at the Museo Carmen Funes. Muscles and their properties were based on comparisons with living animals the final model had a mass of 83 tonnes (91 short tons). Using computer simulation and machine learning techniques, which found a combination of movements that minimised energy requirements, the digital Argentinosaurus learned to walk. The optimal gait found by the algorithms was close to a pace (forelimb and hind limb on the same side of the body move simultaneously). [15] The model reached a top speed of just over 2 m/s (7.2 km/h, 5 mph). [52] The authors concluded with its giant size, Argentinosaurus reached a functional limit. Much larger terrestrial vertebrates might be possible but would require different body shapes and possibly behavioural change to prevent joint collapse. The authors of the study cautioned the model is not fully realistic and too simplistic, and that it could be improved in many areas. For further studies, more data from living animals is needed to improve the soft tissue reconstruction, and the model needs to be confirmed based on more complete sauropod specimens. [15]

Argentinosaurus was discovered in the Argentine Province of Neuquén. It was originally reported from the Huincul Group of the Río Limay Formation, [2] which have since become known as the Huincul Formation and the Río Limay Subgroup, the latter of which is a subdivision of the Neuquén Group. This unit is located in the Neuquén Basin in Patagonia. The Huincul Formation is composed of yellowish and greenish sandstones of fine-to-medium grain, some of which are tuffaceous. [53] These deposits were laid down during the Upper Cretaceous, either in the middle Cenomanian to early Turonian stages [54] or the early Turonian to late Santonian. [55] The deposits represent the drainage system of a braided river. [56]

Fossilised pollen indicates a wide variety of plants was present in the Huincul Formation. A study of the El Zampal section of the formation found hornworts, liverworts, ferns, Selaginellales, possible Noeggerathiales, gymnosperms (including gnetophytes and conifers), and angiosperms (flowering plants), in addition to several pollen grains of unknown affinities. [57] The Huincul Formation is among the richest Patagonian vertebrate associations, preserving fish including dipnoans and gar, chelid turtles, squamates, sphenodonts, neosuchian crocodilians, and a wide variety of dinosaurs. [54] [58] Vertebrates are most commonly found in the lower, and therefore older, part of the formation. [59]

In addition to Argentinosaurus, the sauropods of the Huincul Formation are represented by another titanosaur, Choconsaurus, [60] and several rebbachisaurids including Cathartesaura, [61] Limaysaurus, [62] [63] and some unnamed species. [59] Theropods including carcharodontosaurids such as Mapusaurus, [51] abelisaurids including Skorpiovenator, [64] Ilokelesia, and Tralkasaurus, [65] noasaurids such as Huinculsaurus, [66] paravians such as Overoraptor, [67] and other theropods such as Aoniraptor and Gualicho [68] have also been discovered there. [54] Several iguanodonts are also present in the Huincul Formation. [53]

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Genomes of Herbaceous Land Plants

Yuannian Jiao , Hui Guo , in Advances in Botanical Research , 2014

7 Overview of Genomic Analyses in Gymnosperms

The spermatophytes (seed plants), which include gymnosperms and angiosperms, are some of the most important organisms on Earth. Angiosperms are the most diverse and widely studied seed plants. Large-scale phylogenetic analyses have identified complex patterns of diversification ( Bell, Soltis, & Soltis, 2010 Magallon & Castillo, 2009 Smith, Beaulieu, Stamatakis, & Donoghue, 2011 ), and numerous genomes have been fully, or at least partially, sequenced. Gymnosperms are a group of seed-producing plants that include conifers, cycads, Ginkgo and Gnetales, with fewer than 1000 extant species (compared to about 300,000 extant angiosperms). By far, the largest group of living gymnosperms is the conifers (pines, cypresses and relatives). Compared to angiosperms, little is known about the patterns of diversification and genome evolution in gymnosperms, and there is no sequenced genome in this clade so far.

Many gymnosperms have exceptionally large genomes, partly accounting for their limited genomic resources. For example, conifer genome sizes range from 18 to 35 Gb ( Murray, Leitch, & Bennett, 2012 ), which has hindered whole-genome sequencing. The huge genome size is of interest, because it has been suggested that polyploidy is rare among gymnosperms ( Delevoryas, 1979 ). Recent efforts have elucidated that the large genome size might be associated with rapid expansion of retrotransposons and may be limited to conifers, Pinaceae ( Grotkopp, Rejmanek, Sanderson, & Rost, 2004 Hall, Dvorak, Johnston, Price, & Williams, 2000 Kovach et al., 2010 Morse et al., 2009 Wakamiya, Newton, Johnston, & Price, 1993 ). A recent study suggested elevated rates of genome size and diversification within the last 100 million years, especially in Pinus ( Burleigh, Barbazuk, Davis, Morse, & Soltis, 2012 ).

Although there is not yet a completed gymnosperm genome sequence, large-scale transcriptome data have been generated and deposited in public databases such as GenBank and PlantGDB. Large-insert BAC genomic libraries have been constructed for P. pinaster, P. glauca and P. taeda ( Bautista et al., 2007 Hamberger et al., 2009 Magbanua et al., 2011 ). By sequencing BACs, it has been proposed that pseudogene formation may be a frequent feature within conifer genomes ( Kovach et al., 2010 Magbanua et al., 2011 ). Very large amounts of repetitive DNAs are in conifer genomes as well ( Magbanua et al., 2011 Morse et al., 2009 ), consistent with their large genome sizes. Given the taxonomic position, ecological and economic significance of conifers, several research groups have been funded to sequence whole conifer genomes, including pines, spruces and Douglas fir in the last few years. A European consortium led by Sweden is sequencing the genome of Norway spruce ( Nystedt et al., 2013 ). A USDA-funded project was launched to sequence the genomes of loblolly pine (P. taeda), Douglas fir (P. menziesii) and sugar pine (P. lambertiana) ( http://www.pinegenome.org/pinerefseq/ ). A Genome Canada project is sequencing the white spruce (P. glauca) genome ( http://www.smartforests.ca/en-ca/home.aspx ). These genomes will provide important resources for better understanding of plant evolution and function, enhancing and protecting the word's conifer forests.

One of the most long-standing and controversial issues in gymnosperm systematics is the phylogenetic position of Gnetales ( Burleigh & Mathews, 2004 Chaw, Parkinson, Cheng, Vincent, & Palmer, 2000 Donoghue & Doyle, 2000 Mathews, 2009 Zhong et al., 2011 Zhong, Yonezawa, Zhong, & Hasegawa, 2010 ), a morphologically and ecologically diverse group of gymnosperms. The gnetophytes have vessel elements such as those found in flowering plants, which transport water within the plant. The Gnetales were initially thought to be the nearest relatives of flowering plants (angiosperms) based on morphological similarities ( Fig. 9.2 A ), an idea called the ‘anthophyte’ hypothesis ( Crane, 1985 Doyle & Donoghue, 1986 Rothwell & Serbet, 1994 ). However, all recent molecular evolutionary evidence is against this hypothesis, although failing to reach a final conclusion about the phylogenetic placement of Gnetales ( Burleigh & Mathews, 2004 Zhong et al., 2011 ). There are three different hypotheses somewhat supported by molecular analysis for the position of Gnetales: (1) as sister group to all conifers (the ‘Gnetifer’ hypothesis— Fig. 9.2 B Chaw et al., 2000 ) (2) within conifers, close to Pinaceae (the ‘Gnepine’ hypothesis— Fig. 9.2 C Bowe, Coat, & dePamphilis, 2000 Chaw et al., 2000 Hajibabaei, Xia, & Drouin, 2006 Wu, Wang, Liu, & Chaw, 2007 Zhong et al., 2010 ) (3) within conifers, but sister to Cupressophyta (non-Pinaceae conifers the ‘Gnecup’ hypothesis— Fig. 9.2 D Doyle, 2006 Nickrent, Parkinson, Palmer, & Duff, 2000 ). Zhong et al. evaluated the robustness of several systematic errors in seed plant phylogenomic inferences, including taxon sampling, long-branch attraction (LBA) ( Felsenstein, 1978 Hendy & Penny, 1989 ) and parallel substitutions. It has been proposed that improved taxon sampling was not sufficient to overcome LBA between Curessophytes and Gnetales ( Wu, Wang, Hsu, Lin, & Chaw, 2011 Zhong et al., 2011 ). These controversial results from chloroplast genomes might be solved by the conifer nuclear genomes that are being sequenced as noted in the preceding text.

Figure 9.2 . Four different hypotheses regarding the phylogenetic position of Gnetales. (A) The ‘anthophyte’ hypothesis: Gnetales is sister to angiosperms. (B) The ‘Gnetifer’ hypothesis: Gnetales is sister to conifers as a whole. (C) The ‘Gnepine’ hypothesis: Gnetales is sister to Pinaceae, which has relatively more support from molecular analyses. (D) The ‘Gnecup’ hypothesis: Gnetales is sister to Cupressophyta (non-Pinaceae conifers).


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