Abstract Phylogenetic methods have long been used in biology and more recently have been extended to other fields—for example, linguistics and technology—to study evolutionary histories. Galaxies ...also have an evolutionary history and fall within this broad phylogenetic framework. Under the hypothesis that chemical abundances can be used as a proxy for the interstellar medium’s DNA, phylogenetic methods allow us to reconstruct hierarchical similarities and differences among stars—essentially, a tree of evolutionary relationships and thus history. In this work, we apply phylogenetic methods to a simulated disk galaxy obtained with a chemodynamical code to test the approach. We found that at least 100 stellar particles are required to reliably portray the evolutionary history of a selected stellar population in this simulation, and that the overall evolutionary history is reliably preserved when the typical uncertainties in the chemical abundances are smaller than 0.08 dex. The results show that the shapes of the trees are strongly affected by the age–metallicity relation, as well as the star formation history of the galaxy. We found that regions with low star formation rates produce shorter trees than regions with high star formation rates. Our analysis demonstrates that phylogenetic methods can shed light on the process of galaxy evolution.
ABSTRACT
Stellar chemical abundances have proved themselves a key source of information for understanding the evolution of the Milky Way, and the scale of major stellar surveys such as GALAH have ...massively increased the amount of chemical data available. However, progress is hampered by the level of precision in chemical abundance data as well as the visualization methods for comparing the multidimensional outputs of chemical evolution models to stellar abundance data. Machine learning methods have greatly improved the former; while the application of tree-building or phylogenetic methods borrowed from biology are beginning to show promise with the latter. Here, we analyse a sample of GALAH solar twins to address these issues. We apply The Cannon algorithm to generate a catalogue of about 40 000 solar twins with 14 high precision abundances which we use to perform a phylogenetic analysis on a selection of stars that have two different ranges of eccentricities. From our analyses, we are able to find a group with mostly stars on circular orbits and some old stars with eccentric orbits whose age–Y/Mg relation agrees remarkably well with the chemical clocks published by previous high precision abundance studies. Our results show the power of combining survey data with machine learning and phylogenetics to reconstruct the history of the Milky Way.
The most metal-poor stars provide valuable insights into the early chemical enrichment history of a system, carrying the chemical imprints of the first generations of supernovae. The most metal-poor ...region of the Sagittarius dwarf galaxy remains inadequately observed and characterised. To date, only $ stars with $ have been chemically analysed with high-resolution spectroscopy. In this study, we present the most extensive chemical abundance analysis of 12 low-metallicity stars with metallicities down to $ and located in the main body of Sagittarius. These targets, selected from the Pristine Inner Galaxy Survey, were observed using the MIKE high-resolution spectrograph at the Magellan-Clay telescope, which allowed us to measure up to 17 chemical species. The chemical composition of these stars reflects the imprint of a variety of type II supernovae (SNe II). A combination of low- to intermediate-mass high-energy SNe and hypernovae ($ is required to account for the abundance patterns of the lighter elements up to the Fe-peak. The trend of the heavy elements suggests the involvement of compact binary merger events and fast-rotating (up to $ intermediate-mass to massive metal-poor stars ($ that are the sources of rapid and slow processes, respectively. Additionally, asymptotic giant branch stars contribute to a wide dispersion of Ba/Mg and Ba/Eu . The absence of an $ in our data indicates that type Ia supernovae did not contribute in the very metal-poor region ($ However, they might have started to pollute the interstellar medium at $ given the relatively low Co/Fe in this metallicity region.
The most metal-poor stars provide valuable insights into the early chemical enrichment history of a system, carrying the chemical imprints of the first generations of supernovae. The most metal-poor ...region of the Sagittarius dwarf galaxy remains inadequately observed and characterised. To date, only \(\sim4\) stars with Fe/H~\(<-2.0\) have been chemically analysed with high-resolution spectroscopy. In this study, we present the most extensive chemical abundance analysis of 12 low-metallicity stars with metallicities down to Fe/H~\(=-3.26\) and located in the main body of Sagittarius. These targets, selected from the Pristine Inner Galaxy Survey, were observed using the MIKE high-resolution spectrograph at the {\it Magellan-Clay} telescope, which allowed us to measure up to 17 chemical species. The chemical composition of these stars reflects the imprint of a variety of type~II supernovae (SNe~II). A combination of low- to intermediate-mass high-energy SNe and hypernovae (\(\sim10-70\msun\)) is required to account for the abundance patterns of the lighter elements up to the Fe-peak. The trend of the heavy elements suggests the involvement of compact binary merger events and fast-rotating (up to \(\sim300\kms\)) intermediate-mass to massive metal-poor stars (\(\sim25-120\msun\)) that are the sources of rapid and slow processes, respectively. Additionally, asymptotic giant branch stars contribute to a wide dispersion of Ba/Mg and Ba/Eu. The absence of an \(\alpha-\)knee in our data indicates that type Ia supernovae did not contribute in the very metal-poor region (Fe/H~\(\leq-2.0\)). However, they might have started to pollute the interstellar medium at Fe/H~\(>-2.0\), given the relatively low Co/Fe in this metallicity region.
Phylogenetic methods have long been used in biology, and more recently have been extended to other fields - for example, linguistics and technology - to study evolutionary histories. Galaxies also ...have an evolutionary history, and fall within this broad phylogenetic framework. Under the hypothesis that chemical abundances can be used as a proxy for interstellar medium's DNA, phylogenetic methods allow us to reconstruct hierarchical similarities and differences among stars - essentially a tree of evolutionary relationships and thus history. In this work, we apply phylogenetic methods to a simulated disc galaxy obtained with a chemo-dynamical code to test the approach. We found that at least 100 stellar particles are required to reliably portray the evolutionary history of a selected stellar population in this simulation, and that the overall evolutionary history is reliably preserved when the typical uncertainties in the chemical abundances are smaller than 0.08 dex. The results show that the shape of the trees are strongly affected by the age-metallicity relation, as well as the star formation history of the galaxy. We found that regions with low star formation rates produce shorter trees than regions with high star formation rates. Our analysis demonstrates that phylogenetic methods can shed light on the process of galaxy evolution.
Schistosoma turkestanicum is a parasitic blood fluke widely distributed across Asia. Infection with S.turkestanicum in mammals, including domestic livestock, causes the debilitating disease ...schistosomiasis and although this parasite is not known to complete a full lifecycle in a human host it is a causative agent of cercarial dermatitis(CD) and a potential agent of neuroschistosomiasis. In 2010 a natural focus of this parasite was reported infecting Red deer in the Gemenc region of Hungary and prior molecular clock analyses places the population in this region around the time of the last ice age. So far only a few geographic isolates have been sequenced for this parasite limiting our understanding of the routes of transmission of this pathogen and there is no literature review collating known geographic localities, current and historic, which may shed light on the distribution of S.turkestanicum. There have also been few studies on the phylogeography of the intermediate host vector of this parasite, the fresh water snail Radix auricularia, where the presence of this species determines the location of transmission sites. Presently there is no vaccine to protect humans or livestock from infection with S.turkestanicum, or any other schistosome species of medical importance, and no vaccine candidates have been characterised or proposed for this species. Advances in computational methods of sequence annotation, structural prediction and antigenic characterisation enable rapid comparison of potential vaccine target antigens to predict vaccine efficacy before testing in vivo. Currently many schistosome genomes, including S.turkestanicum, are not annotated, hindering the screening of these genomes for potential vaccine candidates. Additionally, there have been few studies on the population dynamics of potential Schistosome vaccine candidate proteins where the diversity and accelerated evolution of antigenic proteins within a population is hypothesised to be responsible for the current lack in efficacy of Schistosome vaccine candidates. 6 In this thesis population and molecular clock analyses were carried out on S.turkestanicum and their intermediate hosts R.auricularia, from multiple geographic localities to track the historic spread of this Asian parasite to Europe. The results of this study identified the introduction of S.turkestanicum in Hungary likely followed the introduction of R.auricularia, around 316,000 YA. Furthermore transmission of S.turkestanicum occurred multiple times in the past between Hungary, the Middle-East and China however intermediate host population movement was much more conservative, with only one predicted colonisation dated at around 420,000 YA and a potential isolation event separating Asian and European localities. This ancient restriction of movement could be a result of geographic barriers preventing gene flow which divide Europe and Asia. An extensive literature review on S.turkestanicum revealed the presence of this parasite in 14 different mammalian species in 14 localities ranging from central Europe to the Russian Far East and highlighted a lack of study of infection prevalence in wild mammals and a lack of recent studies in Middle and Far-Eastern regions. Additionally, in the absence of whole genome annotations for multiple schistosome species, including S.turkestanicum, an annotation pipeline was developed to predict putative orthologous proteins and plot antigenicity to aid in the evaluation of these proteins as vaccine candidates. Potential vaccine candidates, such as Schistosome Tetraspanin Orphan Receptor (St-TOR), Tetraspanin-1 (Tsp1), Tetraspanin-2 (Tsp2), Tetraspanin-23 (Tsp23), as well as one candidate which has been less well studied, CD63-like protein, were successfully predicted and further subject to population analyses in the S.turkestanicum population. The large extracellular regions (LEL) used as vaccine candidates in clinical trials for schistosome vaccines, were found to be the most variable regions between schistosome species where gene divergence of Tsp23 LEL, CD63-like LEL and STOR ED-1 peptide corresponds to species divergence suggesting the possibility that host-parasite interaction proteins may drive speciation in schistosomes. The observation of a number of DNA artefacts in otherwise high scoring sequence regions across the vaccine candidate datasets lead to the development of the Basecap program to help prevent the incorporation of error as real SNP's into later population and functional 7 analyses using Sanger sequences. The use of Basecap led to a dramatic reduction in diversity for the schistosome vaccine candidate CD63-like LEL and highlights the importance of read merging methods based on score as well as manual inspection of SNPs within a population. Most artefacts in all 3 test datasets led to the interpretation of non-synonymous changes into the sequence data and notably Tajima's D estimates were found to be highly sensitive to these artefacts which could have large implications for functional studies. Inter-host sequencing of these potential vaccine candidates identified variation within the S.turkestanicum population in the functional LEL regions of Tsp23 and CD63-like protein. Reverse vaccinology methods predicted immune epitope regions at variable sites and these variable sites included both neutral variants and variants predicted to be under balancing selection. This suggests that parasite diveristy in the potential vaccine candidate regions Tsp23 and CD63-like protein LEL regions may be maintained by frequency dependant selection, thowing into question their suitability as vaccine candidates. Conversely, there was no diversity observed for ED1 peptide region of S.turkestanicum in Hungary and further sequencing identified a completed lack of diversity in geographic isolates, from different host species, suggesting that the function of the ED1 peptide may be highly conserved between individuals in multiple host species and in different geographic localities. The function of St-TOR as an immune-modulator may complicate its use as a candidate, however, the lack of variation observed in this study, in combination with the prediction of only a single expressed transcript suggests that the St-TOR ED1 peptide could be an ideal vaccine candidate for S.turkestanicum. The functions of host-parasite interaction proteins in schistosomes warrant further study, for example it would be interesting to explore the potential role of cholesterol in tetraspanin protein function and the CD63-like protein could represent an interesting therapeutic target for inflammatory diseases with a putative IL-10 regulatory function.
Abstract
Molluscs are a highly speciose phylum that exhibits an astonishing array of colours and patterns, yet relatively little progress has been made in identifying the underlying genes that ...determine phenotypic variation. One prominent example is the land snail
Cepaea nemoralis
for which classical genetic studies have shown that around nine loci, several physically linked and inherited together as a ‘supergene’, control the shell colour and banding polymorphism. As a first step towards identifying the genes involved, we used whole-genome resequencing of individuals from a laboratory cross to construct a high-density linkage map, and then trait mapping to identify 95% confidence intervals for the chromosomal region that contains the supergene, specifically the colour locus (
C
), and the unlinked mid-banded locus (
U
). The linkage map is made up of 215,593 markers, ordered into 22 linkage groups, with one large group making up ~27% of the genome. The
C
locus was mapped to a ~1.3 cM region on linkage group 11, and the
U
locus was mapped to a ~0.7 cM region on linkage group 15. The linkage map will serve as an important resource for further evolutionary and population genomic studies of
C. nemoralis
and related species, as well as the identification of candidate genes within the supergene and for the mid-banding phenotype.
Stellar chemical abundances have proved themselves a key source of information for understanding the evolution of the Milky Way, and the scale of major stellar surveys such as GALAH have massively ...increased the amount of chemical data available. However, progress is hampered by the level of precision in chemical abundance data as well as the visualization methods for comparing the multidimensional outputs of chemical evolution models to stellar abundance data. Machine learning methods have greatly improved the former; while the application of tree-building or phylogenetic methods borrowed from biology are beginning to show promise with the latter. Here we analyse a sample of GALAH solar twins to address these issues. We apply The Cannon algorithm to generate a catalogue of about 40,000 solar twins with 14 high precision abundances which we use to perform a phylogenetic analysis on a selection of stars that have two different ranges of eccentricities. From our analyses we are able to find a group with mostly stars on circular orbits and some old stars with eccentric orbits whose age-Y/Mg relation agrees remarkably well with the chemical clocks published by previous high precision abundance studies. Our results show the power of combining survey data with machine learning and phylogenetics to reconstruct the history of the Milky Way.
The koala, the only extant species of the marsupial family Phascolarctidae, is classified as 'vulnerable' due to habitat loss and widespread disease. We sequenced the koala genome, producing a ...complete and contiguous marsupial reference genome, including centromeres. We reveal that the koala's ability to detoxify eucalypt foliage may be due to expansions within a cytochrome P450 gene family, and its ability to smell, taste and moderate ingestion of plant secondary metabolites may be due to expansions in the vomeronasal and taste receptors. We characterized novel lactation proteins that protect young in the pouch and annotated immune genes important for response to chlamydial disease. Historical demography showed a substantial population crash coincident with the decline of Australian megafauna, while contemporary populations had biogeographic boundaries and increased inbreeding in populations affected by historic translocations. We identified genetically diverse populations that require habitat corridors and instituting of translocation programs to aid the koala's survival in the wild.
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