Using BioPython to analyze sequence alignments

University of Illinois at Urbana-Champaign. Graduate College. Focal Point InitiativeOpe

Underrepresented Populations at the Archaic Introgression Frontier

Recent advancements in the recovery of ancient genomes have yielded high-coverage sequences for two archaic human species: Neanderthals and Denisovans. Perhaps more surprisingly, direct comparisons of archaic and modern human genomes have revealed a complex landscape of admixture between both archaic species and modern humans (Browning et al., 2018; Villanea and Schraiber, 2019). While we call these regions of the human genome &ldquo;archaically introgressed&rdquo;, they are functional contributors to the living human gene pool, affecting our health and fitness. For Neanderthals in particular, early archaic ancestry maps focused on modern Eurasians, as hundreds of genomes from Europe and East Asia were readily available from the 1000 Genomes Project (see Sankararaman et al., 2014; Vernot and Akey, 2014). Coupled with the geographic distribution of Neanderthal archaeological sites, which are largely located in Europe, this created a strong impression to the larger public that individuals of European descent, in particular, carried archaic genomic elements, which coincided with a larger interest in commodifying archaic ancestry by personalized genomic companies&mdash;as evidenced by 23 and Me incorporating a report of Neanderthal ancestry into their mainline product. &nbsp;</p

The Importance of Nebular Continuum and Line Emission in Observations of Young Massive Star Clusters

In this spectroscopic study of infant massive star clusters, we find that continuum emission from ionized gas rivals the stellar luminosity at optical wavelengths. In addition, we find that nebular line emission is significant in many commonly used broad-band HST filters including the F814W I-band, the F555W V-band and the F435W B-band. Two young massive clusters (YMCs) in NGC 4449 were targeted for spectroscopic observations after Reines et al. (2008a) discovered an F814W I-band excess in their photometric study of radio-detected clusters in the galaxy. The spectra were obtained with the Dual Imaging Spectrograph on the 3.5 m APO telescope. We supplement these data with HST and SDSS photometry. By comparing our data to the Starburst99 and GALEV models, we find that nebular continuum emission competes with the stellar light in our observations and that the relative contribution is largest in the U- and I-bands, where the Balmer and Paschen jumps are located. The spectra also exhibit strong line emission including the [SIII] 9069,9532 lines in the HST F814W I-band. We find that the combination of nebular continuum and line emission can account for the F814W I-band excess found by Reines et al. (2008a). In an effort to provide a benchmark for estimating the impact of ionized gas emission on photometric observations of YMCs, we compute the relative contributions of the stellar continuum, nebular continuum, and emission lines to the total flux of a 3 Myr-old cluster through various HST filter/instrument combinations, including filters in the WFC3. We urge caution when comparing observations of YMCs to evolutionary synthesis models since nebular emission can have a large impact on magnitudes and colors of young (< 5 Myr) clusters, significantly affecting inferred properties such as ages, masses and extinctions. (Abridged)Comment: 13 pages, 11 figures, Accepted for Publication in Ap

Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture

The archaic ancestry present in the human genome has captured the imagination of both scientists and the wider public in recent years. This excitement is the result of new studies pushing the envelope of what we can learn from the archaic genetic information that has survived for over 50,000 years in the human genome. Here, we review the most recent ten years of literature on the topic of archaic introgression, including the current state of knowledge on Neanderthal and Denisovan introgression, as well as introgression from other as-yet unidentified archaic populations. We focus this review on four topics: 1) a reimagining of human demographic history, including evidence for multiple admixture events between modern humans, Neanderthals, Denisovans, and other archaic populations; 2) state-of-the-art methods for detecting archaic ancestry in population-level genomic data; 3) how these novel methods can detect archaic introgression in modern African populations; and 4) the functional consequences of archaic gene variants, including how those variants were co-opted into novel function in modern human populations. The goal of this review is to provide a simple-to-access reference for the relevant methods and novel data, which has changed our understanding of the relationship between our species and its siblings. This body of literature reveals the large degree to which the genetic legacy of these extinct hominins has been integrated into the human populations of today. &nbsp;</p

Emerging Massive Star Clusters Revealed: High Resolution Imaging of NGC 4449 from the Radio to the Ultraviolet

We present a multi-wavelength study of embedded massive clusters in the nearby (3.9 Mpc) starburst galaxy NGC 4449 in an effort to uncover the earliest phases of massive cluster evolution. By combining high resolution imaging from the radio to the ultraviolet, we reveal these clusters in the process of emerging from their gaseous and dusty birth cocoons. We use Very Large Array (VLA) observations at centimeter wavelengths to identify young clusters surrounded by ultra-dense HII regions, detectable via their production of thermal free-free radio continuum. Ultraviolet, optical and infrared observations are obtained from the Hubble and Spitzer Space Telescope archives for comparison. We detect 39 compact radio sources towards NGC 4449 at 3.6 cm using the highest resolution (1.3") and sensitivity (RMS ~ 12 uJy) VLA image of the galaxy to date. We reliably identify 13 thermal radio sources and their physical properties are derived using both nebular emission from the HII regions and SED fitting to the stellar continuum. These radio detected clusters have ages < 5 Myr and stellar masses of order 10^4 Msun. The measured extinctions are quite low: 12 of the 13 thermal radio sources have Av < 1.5, while the most obscured source has Av ~ 4.3. By combining results from the nebular and stellar emission, we find an I-band excess that is anti-correlated with cluster age and an apparent mass-age correlation. Additionally, we find evidence that local processes such as supernovae and stellar winds are likely playing an important role in triggering the current bursts of star formation within NGC 4449.Comment: Accepted for publication in the Astronomical Journal. 20 pages, 14 figure

Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma

Despite the histological similarity of ependymomas from throughout the neuroaxis, the disease likely comprises multiple independent entities, each with a distinct molecular pathogenesis. Transcriptional profiling of two large independent cohorts of ependymoma reveals the existence of two demographically, transcriptionally, genetically, and clinically distinct groups of posterior fossa (PF) ependymomas. Group A patients are younger, have laterally located tumors with a balanced genome, and are much more likely to exhibit recurrence, metastasis at recurrence, and death compared with Group B patients. Identification and optimization of immunohistochemical (IHC) markers for PF ependymoma subgroups allowed validation of our findings on a third independent cohort, using a human ependymoma tissue microarray, and provides a tool for prospective prognostication and stratification of PF ependymoma patients

Ancient DNA suggests modern wolves trace their origin to a late Pleistocene expansion from Beringia.

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographic distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single late Pleistocene population. Both the geographic origin of this ancestral population and how it became widespread remain unknown. Here, we used a spatially and temporally explicit modelling framework to analyse a dataset of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore, and provides an insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.L.L., K.D. and G.L. were supported by the Natural Environment Research Council, UK (grant numbers NE/K005243/1, NE/K003259/1); LL was also supported by the European Research Council grant (339941‐ADAPT); A.M. and A.E. were supported by the European Research Council Consolidator grant (grant number 647787‐LocalAdaptation); L.F. and G.L. were supported by the European Research Council grant (ERC‐2013‐StG 337574‐UNDEAD); T.G. was supported by a European Research Council Consolidator grant (681396‐Extinction Genomics) & Lundbeck Foundation grant (R52‐5062); O.T. was supported by the National Science Center, Poland (2015/19/P/NZ7/03971), with funding from EU's Horizon 2020 programme under the Marie Skłodowska‐Curie grant agreement (665778) and Synthesys Project (BETAF 3062); V.P., E.P. and P.N. were supported by the Russian Science Foundation grant (N16‐18‐10265 RNF); A.P. was supported by the Max Planck Society; M.L‐G. was supported by a Czech Science Foundation grant (GAČR15‐06446S)

Ancient DNA suggests modern wolves trace their origin to a late Pleistocene expansion from Beringia.

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographic distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single late Pleistocene population. Both the geographic origin of this ancestral population and how it became widespread remain unknown. Here, we used a spatially and temporally explicit modelling framework to analyse a dataset of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore, and provides an insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.L.L., K.D. and G.L. were supported by the Natural Environment Research Council, UK (grant numbers NE/K005243/1, NE/K003259/1); LL was also supported by the European Research Council grant (339941‐ADAPT); A.M. and A.E. were supported by the European Research Council Consolidator grant (grant number 647787‐LocalAdaptation); L.F. and G.L. were supported by the European Research Council grant (ERC‐2013‐StG 337574‐UNDEAD); T.G. was supported by a European Research Council Consolidator grant (681396‐Extinction Genomics) & Lundbeck Foundation grant (R52‐5062); O.T. was supported by the National Science Center, Poland (2015/19/P/NZ7/03971), with funding from EU's Horizon 2020 programme under the Marie Skłodowska‐Curie grant agreement (665778) and Synthesys Project (BETAF 3062); V.P., E.P. and P.N. were supported by the Russian Science Foundation grant (N16‐18‐10265 RNF); A.P. was supported by the Max Planck Society; M.L‐G. was supported by a Czech Science Foundation grant (GAČR15‐06446S)