It is important that gametes have half the amount of DNA Haploid Containing one copy of each chromosome. Human gametes egg and sperm cells are haploid, containing 22 autosomes and one sex chromosome. Errors can occur during meiosis producing gametes with an extra or missing chromosome. The consequences of this following fertilisation depend on which chromosomes are affected.
Click on the different category headings to find out more. You can also change some of your preferences. At the end of meiosis, each resulting haploid cell will contain one of four chromosomes. Two of the four cells will contain one recombinant chromosome. Somatic cells non-sex cells undergo mitosis to produce two distinct cells with identical genetic material. As such, any crossover that occurs between homologous chromosomes in mitosis does not produce a new combination of genes.
Crossing over that occurs in non-homologous chromosomes can produce a type of chromosome mutation known as a translocation. A translocation happens when a chromosome segment detaches from one chromosome and moves to a new position on another non-homologous chromosome. This type of mutation can be dangerous as it often leads to the development of cancer cells.
Prokaryotic cells , like bacteria which are unicellular with no nucleus, also undergo genetic recombination. Although bacteria most commonly reproduce by binary fission, this mode of reproduction does not produce genetic variation. In bacterial recombination, genes from one bacterium are incorporated into the genome of another bacterium through crossing over. Bacterial recombination is accomplished by the processes of conjugation, transformation, or transduction. In conjugation, one bacterium connects itself to another through a protein tube structure called a pilus.
Genes are transferred from one bacterium to the other through this tube. In transformation, bacteria take up DNA from their environment. The DNA remnants in the environment most commonly originate from dead bacterial cells. A PHI test was also performed within and between determined groups and p -values for each comparison are presented in Table 1. Table 1. Concatenated sequences are based on five housekeeping genes.
From E. The remaining 97 E. Several isolates, representing one sequence type from the same geographical origin, are shown by a circle with a single color, whereas clonal isolates from different geographical origins were divided into several colors within one circle Figures 1A , 2. Figure 1.
A Split decomposition network of 97 E. Strains are color coded according to the geographic origin described in the legend. Reference strains are identified by black circles. B Histogram representing the total number of E. Figure 2. Overlaid Bayesian consensus trees of 97 E. The root canal tree is shown in blue. Reference strains are identified by black circle outlines. A split decomposition network was constructed from 97 concatenated E.
Reticulations in the graph are clearly present especially noticeable in Group 2 , and are evidence for recombination or other forms of homoplasy between different sequence types. Group 2 is composed of five subgroups, which were defined based on arrangement of sequence types in the network Figure 1A , a hierarchical clustering heat map: Figure S2 , and careful examination of the multiple sequence alignment Figure S3. Several sequence types were excluded from groups due to being recombinants identified by examination of the heat map and multiple sequence alignment marked with blue stars in Figure 1A , Figure S3.
The vast majority of sequence types are placed in equivalent groups between the two analyses, however the STRUCTURE analysis combines subgroup 2A and subgroup 2B, and clusters a few other strains in with those from different groups.
In these cases, the strains tend to have a large proportion of inferred admixture in this case equating to possible recombination , for example, ST 32 and ST 1 appear to show slightly more ancestry with the group equating to subgroup 2E instead of 2D, ST 69 from subgroup 2A clusters with subgroup 2E sequences, however both have evidence of ancestry from both subgroups. Figure 3. Each column represents the inferred ancestry for each sequence type from the five predicted populations.
The groups from the hierarchical clustering and splitstree analysis are noted above the columns. The histogram in Figure 1B represents the total number of E. Sequence type 97 included 17 isolates from West Africa with the reference strain Senegal and one from the Caribbean whereas sequence type 96 included one isolate from East Africa and the reference strain Pokoase from West Africa. The Group 2 worldwide was diverse and composed of 82 unique sequence types from all the sampled geographical areas Figure 1A.
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All of these subgroups with the exception of subgroup 2D have more frequent representation of certain geographical regions in our data. Subgroups 2D is the most geographically diverse subgroup at a regional scale with representatives from each large scale region considered. The majority of the strains in this subgroup are from the Caribbean 23 strains and West Africa 11 strains; Figure 1B.
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Upon close examination of the alignment, some of the sequence types from Southern Africa 39, 40, and 41 and the Indian Ocean 79 and 87 are differentiated simply by gaps caused by lack of coverage at the end of certain gene sequences or by one residue unique to a sequence, likely increasing the representation of their regions in the group in terms of unique sequence types Figure S3. Strains from West Africa and the Caribbean tend to be more genetically diverse within this group.
Notable exceptions to the lack of diversity in Southern African sequence types in this subgroup are sequence type 42, which is recombinant as noted below, and sequence type 32, which is nearly identical to the East African sequence type 1 Kenya , and shares its lip B gene with West African and Caribbean subgroup 2B types 51 and They also share a sucA allele that is otherwise exclusively found in subgroup 2D with two Indian Ocean sequence types 83 and 81 in this subgroup.
Figure 4. Distribution of E. Groups are coded by symbols according to the legend. Subgroup 2E is dominated by Southern African 36 strains , mainly Mozambique, and Indian Ocean isolates 25 strains with a small number of other sequence types from West African or mixed origin.
Two sequence types from Burkina Faso 43, 63 and two sequence types from South Africa 3, 19 corresponding to reference strain Mara were not part of any genetic group as they are recombinant strains Figure 1A. Recombination was identified based on the split decomposition network location usually at the vertices , and examination of the multiple sequences alignment and the heat map for close similarity between the given sequence type and a different subgroup Figure S2.
Several other sequence types 50, 56, 69, 72, and 74 from subgroup 2A and sequence type 42 from subgroup 2D tagged with a blue star in Figure 1A were also identified as recombinants based on combined inspection of the multiple sequence alignment, heat map and split decomposition network Figure 1A , Figures S2, S3.
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The distribution of E. Reviewing the trace files revealed that the ESS of the four linked trees were all less than and the trace plots reveal that they did not converge properly.spunmaconthinkderw.ml
This indicated conflicting signals in our data, which are also illustrated by low branch support values in the maximum likelihood trees Figure S1. In phylogenetics, low branch support can be a quantitative indication of recombination or other forms of homoplasy in the data and is also common for short branches. In this case the conflicting signals are most likely due to recombination events between the analyzed strains given the evidence of mosaic genes in the alignment, the reticulate structure in the split decomposition network Figure 1 and the mixed ancestry exhibited in the STRUCTURE analysis Figure 3.
The overlaying of all the trees produced by the BEAST analysis after discarding for burn-in reveals fuzzy regions in the tree which indicate conflicts in the reconstruction. The ratio of recombination to mutation was estimated as 1. The PHI test on E. Furthermore, recombination analysis between the six genetic groups and subgroups was mostly positive and only intragroup recombination was represented in Table 1.
Examination of the alignment reveals clear mosaicism blocks of multiple residues shared with a different group to the exclusion of other members of the same group in sequence types 63, 43, 19, 42, 3 and all strains in subgroup 2A Figure S3. These are the most obvious events because they are between regions that are divergent that contain several mutations delineating the recombination breakpoints.
The strains in general do not contain many variable sites in the genes used, and there are many possible cases where recombination might transfer single SNPs. In such cases it is difficult to identify the events with certainty because the possibility of homoplasy by convergent mutation exists. The PHI test does not identify recombination breakpoints, but does allow a statistical evaluation of the likelihood of recombination between different sequences regardless of the size of the recombined blocks.
This type of test is advantageous in cases where the sequence similarity is high and there are only a small number of discriminatory SNPs to infer recombination compared to methods that attempt to identify breakpoints at the edges of recombination blocks because it may detect the overall signal of recombination from a series of small events that are undetectable individually. Although STRUCTURE doesn't provide a statistical measure for the likelihood of recombination between sequence types, the analysis does suggest widespread recombination between the five different inferred populations.
Despite the apparent unclear population structure and phylogeography of E. Outgrouping the tree using E. The branches leading to each group are relatively long compared to the branches within the groups, allowing us to infer that the groups were probably isolated from one another for a long time. We also infer the possible geographical locations of the ancient progenitors of the groups based on the geographic distributions of the extant strains: we propose that the Group 1 is ancestrally West African, and that Group 2 originates elsewhere.
The divergence of the two main groups possibly predates the spread of livestock across the continent of Africa with the wave of domestication. The presence of several individual sequence types and all sequence types present in subgroup 2A that represent recombination between Group 1 and Group 2 in West Africa, shows the propensity of these groups to recombine. This allows us to infer a later arrival of subgroup 2D in West Africa long after the split between the two groups otherwise the clusters would be more homogeneous.
Apart from Anaplasma marginale de la Fuente et al. We hypothesize that ancient more than years ago and recent cattle less than years ago movements has shaped E. Recent and ancient cattle movement domestication in Africa, the Caribbean, and the Indian Ocean islands are illustrated in Figure 4. Group 1 and subgroups 2A, 2B, 2D, and 2E present in West Africa are also present in Guadeloupe and Antigua, reflecting the historical movement of cattle from this region to the Caribbean Maillard et al.
Subgroup 2E is predominantly present in Southern Africa and the Indian Ocean, suggesting that the small number of strain types from this group that are present in other locations may be the result of recent cattle movement. Given that all the current known vectors of E. Several studies have reported a South and East genetic break in African mammals Pitra et al.
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