This means that some refined "best-fit" speculative genealogy may be possible, if, as was not unknown, these families intermarried within the relatively tight-knit Methodist community. This was in Abbey Street, Dublin In light of this excerpt, and developing the themes of kinship and potential intermarriages, it will come as no surprise to me if we were to eventually find that: a.
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Indeed, the "Minutes of Methodist Conferences in Ireland," , provide some further clues: Conference page : "Q. Who are the Liquidating Committee? The Dublin Preachers, together with Messrs Who are the Missionary Committee to review the concerns of the Missions at the ensuing Conference?
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Who are the Chapel Building Committee, without whose previous consent obtained in writing no Chapel Possibly the same as Henry of Upper Dominick Street. See II next below. See IV below. Clearly too young to have been father of IV next. Henry died at his house in Abbey Street, Dublin, on 31 December , aged 38 years, after an illness during which he " Park, , aged 60 years. Possibly the next? If married or a widow, perhaps the mother of William above, and perhaps even of Henry???
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From notes I have recently despatched to a descendant:. And two others who may have been related:. There were three burials in the Church Records which were not burials, but instead Confirmations:. Decorators, glass merchants, ironmongers, plumbers, marble and stone merchants, of Dublin. He died in This exceptional olfactory capability is reflected in the number of detectable species-specific duplications SSD observed in the African elephant genome and its subsequent ORs that have putatively retained function.
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In contrast, the dolphin has the smallest number of SSDs, reflecting the diminished role of olfaction after the transition from land to water in the evolutionary history of cetaceans Springer and Gatesy To explore how gene expansion has occurred in the OR gene family, with respect to ecological niche adaptation, we investigated SSD events and the fate of the genes such events give rise to in 94 mammals 58 sequenced genomes and 36 from NGS amplicon sequence data.
These data included species representatives from all superordinal groups. Frugivores sampled in this study come from the orders Chiroptera and Primates. Future deorphaning of OR and odorant molecules may allow a more comprehensive study of mammalian olfactory space, and the role of diet in olfactory evolution.
The Vomeronasal or Jacobson organ VNO is used to detect pheromones: water-soluble chemical signals that trigger a social response in a number of mammals Zhang and Webb This pattern was observed across all statistical analyses and was the best-supported niche to explain observed duplication events. The VNO has previously shown the ability to express OR genes Keller and Vosshall , and it has been demonstrated that pheromones can stimulate olfactory neurons, which suggests a complex interaction between the two sensory modes. Additionally, olfr , olfr , and olfr were also found to be expressed in the mouse VNO, and are postduplication functional OR genes in mice.
Our results indicate that the OR repertoire has not evolved to compensate for the complete loss of a VNO, but rather is augmented by the presence of a functioning one in extant taxa. Further studies into the differential expression of VNO receptor genes in olfactory epithelia, the expression of OR genes in VNO tissue and their potential correlations with OR subgenome evolution may help elucidate the patterns observed here.
Ecological niches of 94 mammals. The ecological niche data for 94 mammals used in this study are displayed. Solitary species have on average twice the number of SSDs compared with social species, with no family in particular showing significant differences to others. This suggests that individual OR gene families may have expanded at similar high rates with respect to sociality, with broader repertoires being adaptive to a solitary lifestyle.
In this case, vocalization or display may be the dominant form of communication. Solitary mammals may need to be more vigilant with respect to prey, predators and mating and as such, an expanded OR repertoire could potentially allow a finer tuned sense of olfaction. An exception to this observation is the African elephant, which shows more OR gene duplication events than any other taxon, despite predominantly living in social groups. Given the importance of light in maintaining circadian rhythm Challet , activity phase in mammals has previously been linked to adaptations in visual perception.
In reduced light, olfaction likely plays an important role in hunting, identifying potential threats and communication with conspecifics for both nocturnal and crepuscular species. While nocturnal mammals showed a lower number of non-functional daughters after SSD in OR family 4 compared with crepuscular and diurnal species, the lack of an observed significant correlation between activity phase and OR gene family expansion through duplication in our data is surprising.
This could be due to different taxa occupying the same ecological niches but at different times. However, when accounting for the percentage of the OR repertoire attributable to SSD, terrestrial mammal OR repertoires have undergone almost three times as much OR gene duplication as volant or aquatic mammals. Terrestrial mammals occupy a variety of different niches, which may be associated with such high rates of gene duplications.
The expansion of OR gene families for terrestrial adaptation can also be observed in the high rate of duplication in Class I OR genes which typically bind water odorants compared to aquatic mammals, suggesting a potential novel usage or cooptimization for this class of gene families in adaptation to a nonaquatic environment, as previously observed in the dog Olender et al.
The relatively small number of OR genes in aquatic mammals would imply relaxed selective pressures on olfactory mechanisms for an aquatic lifestyle. Nonetheless, we observed some duplication of OR genes in aquatic taxa, with a higher rate in the manatee compared to cetacean species, suggesting some putatively retained OR functionality in an aquatic environment. Our findings indicate that the evolution and diversification of the mammalian OR repertoire through SSD large expansions within a specific OR family, or of the OR repertoire as a whole and the retention of function in duplicated OR genes is associated with adaptations to a range of ecological niches.
In addition, solitary mammals have undergone nearly twice as many SSD events as social mammals. However, there were no significant differences observed between rhythmic activity phases with respect to OR gene evolution through SSD. The wide range of different terrestrial ecological niches to which mammals have successfully adapted is reflected in the fact that three times as many OR genes are born through gene duplication in terrestrial mammals compared to volant or aquatic mammals.
In this study, we have shown the utility of using phylogenetically independent SSDs as a means of elucidating how environmental niche adaptation is associated with the evolution of sensory perception. As amplicon sequencing and whole genome sequencing become cheaper and faster, future studies will allow the possibility of further exploring these results.
Higher quality genomes will allow further exploration of the associations between OR gene evolution and ecological niche adaptation, possibly uncovering more functional genes or resolving any instances of incorrectly identified pseudogenes. Such a large set of genomic data will play a huge role in the investigation and understanding of mammalian sensory evolution, shedding more light on the relationship between sensory evolution and niche adaptation. Additionally, the modeling of 3D structures of ORs, and deorphaning of receptor and ligand may also help further explore associations between the role of OR repertoire and ecological niche.
The two PCR products per species were pooled then purified and concentrated using Millipore Centrifugal filter units. The OR gene amplicons were sequenced and assembled for all 14 species supplementary table S1 , Supplementary Material online. Such assembly algorithms use a parameter k to control the assembly of reads into contiguous sequences contigs.
Low values for k increase the chances of successful overlaps, and are more sensitive regarding the assembly of fragments compared to larger values. Larger k values however reduce the risk of incorrect overlaps, and are thus more specific. Two independent k ranges were tested: a low k -value range 20— using SOAPdenovo, which allows a maximum k of , and high k- value ranges using ABySS. As the number of assembled contigs dropped dramatically for higher k values, a range of k -values between and was applied. Assembly parameters and approaches were tested using four species with previously sequenced genomes: Canis familiaris dog , Felis catus domestic cat , Myotis lucifugus little brown bat , and Rhinolophus ferrumequinum greater horseshoe bat to ensure that the NGS data generated was a true representation of the OR subgenome.
As each read represented a potential amplified OR gene sequence, a clustering method was applied in addition to de Bruijn graph assemblers to collapse amplicon data. This allowed reads to join clusters despite potential sequence errors and undetermined nucleotide positions. Consensus sequences were then made for each cluster. To determine which method of sequence reconstruction assembly vs. The clustering and assembly methods were compared based on: Number of unique ORs present in the data;. Olfactory Receptor gene sequences were mined from 58 different sequenced mammalian genomes, covering 17 mammalian orders supplementary table S12 , Supplementary Material online and fig.
As some of the genomes used in this study have not yet been annotated, it is possible that a number of identical redundant contigs were present in the whole genome assemblies, either due to different alleles or multiple copies of the same contiguous sequence, leading to an overestimation of the number of ORs per genome. This length threshold allowed us to identify and include functional ORs from fragmented whole genome assemblies or genomes with long, unresolved sequence regions that did not contain a complete ORF.
An OR gene was treated as non-functional if it contained an in-frame stop codon, insertion or deletion frame-shift mutation. Our computational methods detected functional OR genes, OR genes with a premature stop codon, and truncated or degraded pseudogenes.
Therefore, our counts of OR pseudogenes represent a minimum number of detectable pseudogenes within the genome. These OR genes showed on average This data set consisted of OR data from the 58 fully sequenced mammalian genomes coupled with the assembled gene data from the ten species had no genome sequenced described above 3, OR sequences.
OR sequences were classified and converted to amino acid sequences as described above. As the amplified data represent only a subset rather than the full OR repertoire, analyses were performed with and without the additional 36 taxa i. This allowed us test the robustness of our gene data with respect to additional taxa, niches and sequences. Functional and non-functional OR genes were included in each alignment. As both data sets contained 13 OR families, a total of 26 protein alignments were generated. We counted species-specific OR gene duplication SSD events, whereby OR genes have undergone duplication leading to two or more paralogous genes daughters in a single species alone, that are retained in the genome.
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A node was considered to represent an SSD if it contained two or more leaf nodes, all from the same species fig. Chained sub trees consisting of a single target species were counted as multiple SSD events fig. Under this method of counting duplications, we cannot rule out the possibility of a duplication event in which one daughter gene retains function whilst the other degrades beyond recognition in the genome, and therefore cannot be documented as a duplication event.
go here Although we expect the frequency of such events in extant taxa to be low, the estimates here refer to SSDs resulting in paralogous OR genes daughters that are retained and detectable in the genome, and therefore represent minimum levels of observable OR duplication. Additionally, this method will not recover shared ancestral duplication events. A perl script was used to parse these trees, highlighting instances of SSD while relaying specific information about each gene.
We identified three types of duplication nodes: duplication events where all daughter paralogous genes are functional, duplication events where all daughter genes have since lost their function and duplication events showing a combination of both. With respect to non-functional OR genes that are one of a duplicated pair, it is unknown if function was lost soon after duplication or at a later point in the evolutionary history of that species.
To investigate if duplication was diversifying the OR repertoire, the number of different subfamilies within each OR gene family showing SSD events was determined. These niches imply many different ecological modalities, environmental conditions, and sensory perception repertoires. Species were assigned to each niche according to data from the literature supplementary table S12 , Supplementary Material online and fig. Data was normalized to allow comparisons across niches and comparisons between genes mined from whole genomes and NGS data.
The distribution of SSDs detected in each family was normalized by dividing the number of observed SSDs per family by the total SSDs observed for that species supplementary table S13 , Supplementary Material online, see worked example , and this normalization was also applied to the counts of functional and non-functional daughters.