Mitochondrial DNA- a Tool for Phylogenetic and Biodiversity Search in Equines | OMICS International
The animals loosely termed fish constitute more than half of all known parental care; reproduction in relation to conservation and exploitation of marine fishes;. Visit for more related articles at Journal of Biodiversity & Endangered Species The mt-DNA is particularly useful in inferring phylogenetic relationship .. wild and domestic equids [60,], chicken , fish , rhinoceros , goat . Antigua and Barbuda, Argentina, Armenia, Aruba, Australia, Austria, AZ USA . A comprehensive phylogenetic tree for all major groups of fishes has been .. 3– 10 provide more detail on the relationships within selected.
Studies based on mitogenomic data proliferated to methodically probe conflicting hypotheses of relationship for several groups at diverse taxonomic levels, many times proposing alternative arrangements supporting new clades unsuspected by previous classifications 101112 In spite of their new powerful insights, mitogenomic hypotheses were not universally embraced because they represent information from a single locus, prompting corroboration from additional genomic regions.
Several nuclear DNA markers were subsequently developed and applied to infer bony fish relationships. The most popular ones include 28S ribosomal subunit 141516tmo4c4 1718rhodopsin 1920rag1 and rag2 2122mll 20irbp 23and rnf Using a systematic approach to scan genomic databases, a larger set of nuclear markers became available in 25opening a new window to obtaining large multilocus datasets 25262728 Recent studies using between 10 and 20 of these nuclear markers for a few hundred taxa 272829303166have shown improved resolution of phylogenetic relationship at higher and lower taxonomic levels.
Many but not all of the mitogenomic hypotheses received support from nuclear gene data, but the discovery of new clades continued with increasing taxonomic sampling. Initially identified by letters e. Validation of these groups and their proposed names is pending until a comprehensive study including all taxa is produced. Proliferation of new names is useful for identification of the newly discovered groups, but may create confusion if not systematically organized into a global classification.
Molecular phylogenetic methods e. Attempts to estimate divergence dates among crow-group lineages using this approach e.
The discrepancy is larger when divergence estimates for crown teleost lineages have been based on mitogenomic data e.
Nucleotide saturation, compressing basal branch lengths for mtDNA, and the specific approaches used to apply fossils constraints to calibrate the molecular phylogeny may explain this discordance Other studies based on several nuclear genes and larger sets of fossil calibration points produced divergence dates more consistent with the fossil record 2966but a comprehensive time-tree for osteichthyan diversification is not yet available.
Few basal branching events among osteichthyans remain problematic, for example, the relationships among lungfishes, coelacanths, and tetrapods 454647 In contrast, the basal branching pattern for early extant actinopterygians involving polypteriforms, chondrosteans, lepisosteids, Amia and teleosts have been resolved with confidence based on morphological and DNA sequence evidence Similarly, recent molecular studies based on several nuclear genes 25 consistently support relationships among major teleost groups: Elopomorpha, Osteoglossomorpha and Euteleostei 29 The deeper nodes among euteleosts and percomorphs also could be resolved with confidence with this new set of nuclear markers, but a comprehensive phylogeny including all groups is lacking.
In this study we report phylogenetic results based on a taxonomically comprehensive dataset with DNA sequences for 21 nuclear genes. A dataset with taxa was assembled, including four tetrapod and two chondrichthyan outgroups. Bony fish diversity is represented by genera of ca. Phylogenetic results corroborate many previously established hypotheses, but also provide unprecedented resolution among percomorphs.
The uncertain relationships involving most of the extant diversity of percomorphs is resolved into several well-supported groups and, for the first time, we offer a monophyletic definition for Perciformes. Using a set of 60 calibrations, we also provide the most comprehensive hypothesis to date about the tempo of osteichthyan diversification. Considering the new clades obtained in this study and previously published well-supported clades, we propose a new classification for bony fishes based on the nomenclatural scheme recently proposed by Wiley and Johnson 5.
Our hope is that this explicit proposal will facilitate communication among ichthyologists attempting to chart the rapidly changing landscape of phylogeny and classification of fishes. A total of 21 molecular markers with a genome-wide distribution were examined, the majority of which were developed by EToL using a genomic screen pipeline A total of bony fish taxa were initially targeted for this study and samples were primarily obtained from the tissue repository of the Ichthyology Collection at University of Kansas samples or other collections.
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Of the initial list, samples for 18 taxa either failed to amplify or belonged to duplicate species that were ultimately combined or discarded. Sixty taxa that produced sequence data for one or two genes only were also discarded. Both strands of the mt-DNA are completely transcribed from the promoters in the D-loop.
In addition to the promoter sequences, there are two small regions known as the hyper variable regions I and II HV1 at positions — and HV2 at positions 63— [ 48 ]. The third strand has a base sequence which is complementary to one of the key strands and pairs with it, thus displacing the other main strand in the region. Within that region the configuration is thus a form of triple stranded DNA.
The size of this region varies among animal species, from to 4, base pairs [ 34 ]. The substitution rate in the human D-loop has been estimated to be from 2. D-loops occur in numeral of scrupulous conditions, including in telomeres, in DNA repair and arrangements, and as a semi-stable structure in mitochondrial circular DNA molecules. Researchers at Caltech discovered in that the circular mitochondrial DNA from growing cells included a short segment of three strands which they called a displacement loop [ 50 ].
Phylogeny, Anatomy and Physiology of Ancient Fishes
They found the third strand was a replicated segment of the heavy strand or H-strand of the molecule, which it displaced, and was linked with hydrogen bond to the light strand or L-strand. Since then, it has been shown that the third strand is the initial segment generated by a replication of the heavy strand that has been arrested shortly after initiation of replication and is time and again maintained for some period in that state [ 51 ].
The Dloop occurs in the core non-coding area of the mitochondrial DNA molecule, a segment called the control region or D-loop region. The DLoop region is the major control site for mt-DNA expression since it contains the leading-strand for origin of replication and major promoters for transcription [ 27 ].
The D-loop sequences in particular have been used to establish intra-specific and inter-specific relationships, determine maternal contributions, and trace the origin of modern and ancient animals.
The D-loop or control region, although non-coding, contains binding sites for two transcription factors; three Conserved Sequence Blocks CSBs associated with initiation of replication and the loop strand termination associated sequences, all of which play an important role in the replication of the mitochondrial genome. Replication of the mitochondrial DNA can occur in two different ways, both starting in the D-loop region [ 52 ]. One way continues replication of the heavy strand through a substantial part e.
The more recently reported mode starts at a different origin within the Dloop region and uses coupled-strand replication with simultaneous synthesis of both strands [ 5253 ]. Certain bases within the D-loop region are conserved, but huge parts are exceedingly variable and the region has proven to be useful for the study of the evolutionary history of vertebrates [ 54 ].
The region contains promoters for the transcription of RNA from the two strands of mitochondrial DNA immediately adjacent to the D-loop structure that is coupled with initiation of DNA replication [ 47 ]. The conventional wisdom supposed that D-loops were non-functional leftovers of incomplete replication. The function of the D-loop is not yet understandable, but recent research suggests that it participates in the organization of the mitochondrial nucleoid [ 5556 ].
The partial mt-DNA D-loop region of all the registered horse and pony breeds of India, has been sequenced and submitted in GenBank with following accession numbers: Manipuri ponies Genbank accession no. Analysis revealed 70 Haplotypes in Indian horse and ponies.
Importance of D-loop Non-coding region of the mitochondrial DNA mt-DNAthe Displacement loop D-loop has emerged as a mutational hotspot as it has the ability to accumulate mutations at a high, neutral rate as already stated earlier.
Mutation rates in HVI and HVII are particularly high on an average and there is evidence that the rates differ within the regions as well [ 57 ]. As a result of the high average mutation rates and the deficiency of coding or regulatory sequences in the hyper variable regions, they have turn out to be an immensely valuable source for investigating intra-specific genetic variation and differentiation.
The sequence analysis of these two regions is used not only in forensic analyses, but also in medical diagnosis [ 58 ]. The D-loop contains essential transcription and replication elements and mutations in this region may serve as a prospective sensor for cellular DNA damage and a marker for cancer development.
Phylogenetic relationships and evolutionary history of the reef fish family Labridae.
It plays important role in telomeres also as the T-loop which is completed by the D-loop splice, protects the end of the chromosome from damage [ 59 ].
Most of the ancestral markers are found in the D-Loop. Whenever a mutation occurs in this region, the individual does not die and survives to pass the mutation along to future generations. However, the coding region of the mt- DNA is considered essential for the survival of the individual, so usually, whenever a mutation occurs in this region, it is often lethal and the organism dies.
Thus, mutations which arise in the coding region are usually not passed down to future generations. For this reason, over a period of thousands of years, many mutations accumulate in the D-Loop, but very little are found in the coding region.
Mutations are found at a much lower frequency in the coding region because only the mutations which do not end up being lethal are passed down to future generations. The displacement loop, which makes up 5.
This region contained the highest rate of polymorphisms per kilo base, which was not unexpected since the D-loop is known to be the most highly mutable region of the mitochondrial genome. The D-loop has been classified into three different highly conserved regions among 26 species: The ETAS has been implicated in the termination of heavy H strand synthesis, which is important in the termination of replication. Role of D-loop in genetic diversity, maternal lineage and phylogeny studies Understanding the evolution and genetic diversity of various species and classifying their populations by their evolutionary significance is essential for an appropriate conservation plan to be conceived and carried out for both wild and captive populations [ 60 ].
Mitochondrial mt sequences provide rich sources of data for research in evolutionary biology, population genetics and phylogenetics and has been used in studies of the various species like pigs [ 5 ], Echinococcus [ 61 ], wild and domestic equids [ 6062 - 66 ], chicken [ 67 ], fish [ 68 ], rhinoceros [ 69 ], goat [ 70 ].
The complete mitochondrial DNA mtDNA sequences have been determined from more than Chordata species since the first complete mt-DNA sequences of human determined in [ 16 ] which covered all the classes of Chordata [ 71 - 75 ]. Eight complete mitochondrial DNA mt-DNA sequences of reptile species have been determined, including Alligator mississippiensisCaiman crocodilusIguana iguanaEumes egregiusDinodon micarinatusChelonia mydasChrysemys picta and Pelomedusa subrufa [ 76 ].
The neucleotide nt sequence of mitochondrial DNA mt-DNA of Chinese alligator, Alligator sinensiswas determined using the long-PCR and primer walking methods [ 76 ] and demonstrated that Chinese alligator is most closely related to American alligator among three crocodilian species.
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Molecular studies, using mainly mt-DNA sequences, have identified 9 distinct genotypes within E. The mt-DNA sequences can be used to identify the putative wild progenitors, the number of maternal lineages and their geographic origins.
To some extent it may provide important information on the geographic distribution of diversity within livestock species although the usefulness of mt-DNA sequences data will vary between species, depending on the demographic history of the migration from the center s of domestication. More particularly, mtDNA information supports the conclusion that there were at least five major centers of livestock domestication: The mitochondrial DNA studies in horses have proved to be useful to characterize intra and inter-breed relationships [ 663646683 - 90 ].Herps of Louisiana: Anoles (Ep. 1)
Mitochondrial DNA sequence polymorphism has been used to examine genetic relationship within breeds [ 8591 ], among breeds [ 6486 ], between domestic and wild horse populations [ 65 ] and also to address questions of horse domestication [ 6692 ]. Mitochondrial DNA analysis has been widely used to study wild and domestic equids, mainly due to the evolutionary information that can be drawn from sequence data [ 6062 - 66 ].
Mt-DNA sequences will be the markers of choice for domestication studies as the segregation of a mitochondrial DNA lineage within a livestock population, will only have occurred through the domestication of a wild female or through the incorporation of a female into the domestic stock.
Phenotypic differences among the Northern and Southern Iberian groups of breeds are not explained by population sub-division based on maternal lineages. Northern Iberian ponies which were phenotypically close to British ponies, especially Exmoor, are the result of an introgression rather than population replacement. They further demonstrated that the length of the D-loop varied due to the presence of variable numbers of repeats of eight Base Pairs bp in the large conserved central sequence block of the control region.
The number of repeats differed between 2 and 29 copies, although the majority was in the range of 22 to The total number of bases in the D-loop region was bp, bp and bp. The large central conserved sequence block and small conserved sequence blocks 1, 2 and 3 that are common to other mammals were observed. However, the researchers found that, between conserved sequence blocks 1 and 2 there were tandem repeats of an 8 bp equine-specific sequence TGTGCACC, and the number of tandem repeats differed among individual horses.
Comparing DNA sequences between horse and other mammals, the difference in the D-loop region length is mostly due to the difference in the number of DNA sequences at both extremities.
The similarities of the DNA sequences are in the middle part of the D-loop [ 6 ]. In comparison of the sequences among three Thoroughbred horses, it was determined that the region between tRNA Pro and the large central conserved sequence block was the richest in variation.
Only two different sequences were found, one of which corresponds to that of Ishida et al. Thus, variation was found to be very little, regardless of individuals who apparently originated from three distinct geographical regions. The other sequence differed from the first, but both were certainly more similar to the published sequences of three thorough bred and of a Mongolian Horse than to other equids.
Since the sequences varied considerably within the horse breeds, and since Cheju horses clustered with Mongolian horses as well as with horses from other distant breeds, the authors proposed that the horses on Cheju island were of mixed origin in their maternal lineage, and that they may have been present on the island and were the entity of trade before the Mongolian introduction. In a follow-up study Yang et al. Another phylogenetic analysis was performed by Mirol et al.
Mitochondrial D-loop sequence variation among maternal lineages of the Lipizzan, Arabian, and Thoroughbred horses was determined by Kavar et al. Sixteen maternal lines of the Lipizzan horse were grouped into 13 distinct mitochondrial haplotypes with stable inheritance, and no sequence variation was observed that was potentially attributable to mutation within maternal lines. Historical data about the multiple origin of the Lipizzan breed was supported by the phylogenetic analysis, which produced a dendrogram with three separate branches.
Sequencing of Lipizzans revealed 37 haplotypes [ 95 ]. A comparison of these sequences to sequences of domestic and wild horses from GenBank showed a clustering of Lipizzan haplotypes in the majority of haplotype subgroups present in other domestic horses.
The authors proposed that domestic horses could therefore have arisen either from a single large population or from several populations assuming that strong migrations occurred during the early phase of domestication.
Advantages of mt-DNA over microsatellites are that the mitochondrial genome is exclusively maternally inherited, haploid, and does not undergo recombination and the methods for assessing genetic diversity are similar to those for microsatellites.
Thus, the individuals from one matriline dam line are supposed to share single mt-DNA haplotype. Moreover, the control region of mtDNA D-loop provides a highly informative tool for matrilineal relationship studies within breeds to detect their differentiation and to refer to different founder mares. The drawbacks of mtDNA analyses are that they cannot detect gene flows from males and the overall genomic diversity because mtDNA behaves like a single haplotype of extra-nuclear DNA.
The Arabian Horses in the USA were traced in the maternal line to 34 mares showing 27 haplotypes [ 62 ]. They observed single base differences within two lines which were interpreted as representing alternative fixations of past heteroplasmy, calling into question the traditional assumption that Arabian Horses of the same strain necessarily share a common maternal ancestry. Seventeen haplotypes were found in 19 of the most common matrilineal female families of the Thoroughbred horse [ 85 ].
Another analysis of maternal line variation was performed by Luis et al. Tracing back the maternal lineages revealed that only two different lines have survived and therefore only two haplotypes, only one of which is present in the German population. The reduced number of surviving maternal lineages emphasizes the importance of establishing a conservation plan for this endangered breed [ 91 ].
Mitochondrial D-loop for horses from 25 oriental and European breeds, including American mustangs was sequenced by Jansen et al. A phylogenetic network was constructed that showed that most of the 93 different mt-DNA types grouped into 17 distinct phylogenetic clusters.
Phenotypic differences among the Northern and Southern Iberian groups of breeds are not explained by population subdivision based on maternal lineages. Northern Iberian ponies which are phenotypically close to British ponies, especially Exmoor, are the result of an introgression rather than population replacement.