Chromosome-scale genome assembly of the brown anole (Anolis sagrei), an emerging model species

Rapid technological improvements are democratizing access to high quality, chromosome-scale genome assemblies. No longer the domain of only the most highly studied model organisms, now non-traditional and emerging model species can be genome-enabled using a combination of sequencing technologies and assembly software. Consequently, old ideas built on sparse sampling across the tree of life have recently been amended in the face of genomic data drawn from a growing number of high-quality reference genomes. Arguably the most valuable are those long-studied species for which much is already known about their biology; what many term emerging model species. Here, we report a highly complete chromosome-scale genome assembly for the brown anole, Anolis sagrei – a lizard species widely studied across a variety of disciplines and for which a high-quality reference genome was long overdue. This assembly exceeds the vast majority of existing reptile and snake genomes in contiguity (N50 = 253.6 Mb) and annotation completeness. Through the analysis of this genome and population resequence data, we examine the history of repetitive element accumulation, identify the X chromosome, and propose a hypothesis for the evolutionary history of fusions between autosomes and the X that led to the sex chromosomes of A. sagrei

Analysis of the African coelacanth genome sheds light on tetrapod evolution

It was a zoological sensation when a living specimen of the coelacanth was first discovered in 1938, as this lineage of lobe-finned fish was thought to have gone extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features . Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain, and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues demonstrate the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution

Morphological diversity of single neurons in molecularly defined cell types.

Dendritic and axonal morphology reflects the input and output of neurons and is a defining feature of neuronal types1,2, yet our knowledge of its diversity remains limited. Here, to systematically examine complete single-neuron morphologies on a brain-wide scale, we established a pipeline encompassing sparse labelling, whole-brain imaging, reconstruction, registration and analysis. We fully reconstructed 1,741 neurons from cortex, claustrum, thalamus, striatum and other brain regions in mice. We identified 11 major projection neuron types with distinct morphological features and corresponding transcriptomic identities. Extensive projectional diversity was found within each of these major types, on the basis of which some types were clustered into more refined subtypes. This diversity follows a set of generalizable principles that govern long-range axonal projections at different levels, including molecular correspondence, divergent or convergent projection, axon termination pattern, regional specificity, topography, and individual cell variability. Although clear concordance with transcriptomic profiles is evident at the level of major projection type, fine-grained morphological diversity often does not readily correlate with transcriptomic subtypes derived from unsupervised clustering, highlighting the need for single-cell cross-modality studies. Overall, our study demonstrates the crucial need for quantitative description of complete single-cell anatomy in cell-type classification, as single-cell morphological diversity reveals a plethora of ways in which different cell types and their individual members may contribute to the configuration and function of their respective circuits

Measuring change during intervention using norm-referenced, standardized measures: a comparison of raw scores, standard scores, age equivalents and growth scale values from the Preschool Language Scales-5

Purpose: Norm-referenced, standardized measures are tools designed to characterize a child’s abilities relative to their same-aged peers, but they have also been used to measure changes in skills during intervention. This study compared the psychometric properties of four types of available scores from one commonly used standardized measure, the Preschool Language Scales-5 (PLS-5), to detect changes in children’s language skills during and after a language intervention. Method: This study included data from 110 autistic children ages 18-48 months whose mother participated in an 8-week parent-mediated language intervention. Children’s language skills were measured at three timepoints using the PLS-5. Changes in children’s expressive and receptive language skills were calculated using raw scores, standard scores, age equivalents, and growth scale values (GSVs). Results: Analysis of raw scores, age equivalents, and GSVs indicated significant improvement in autistic children’s scores in both receptive and expressive language throughout the study (i.e., during the intervention period and in the 3-month period after the intervention). Standard scores suggested improvement only in the receptive language scale during the intervention period. Standard scores showed a floor effect for children who scored at -3 SD below the mean. Conclusions: Findings suggested that GSVs were not only psychometrically-sound, but were the most direct, and sensitive measure of changes in skills compared to raw, standard, and age equivalent scores. Floor effects may limit the sensitivity of standard scores to detect changes in children’s skills. Strengths, limitations, and interpretations of each of the scoring approaches in measuring changes in skills during intervention were discussed

Measuring changes in language skills (Kwok et al., 2022)

Purpose: Norm-referenced, standardized measures are tools designed to characterize a child’s abilities relative to their same-age peers, but they also have been used to measure changes in skills during intervention. This study compared the psychometric properties of four types of available scores from one commonly used standardized measure, the Preschool Language Scales–Fifth Edition (PLS-5), to detect changes in children’s language skills during and after a language intervention. Method: This study included data from 110 autistic children aged 18–48 months whose mother participated in an 8-week parent-mediated language intervention. Children’s language skills were measured at 3 time points using the PLS-5. Changes in children’s expressive and receptive language skills were calculated using raw scores, standard scores, age equivalents, and growth scale values (GSVs). Results: Analysis of raw scores, age equivalents, and GSVs indicated significant improvement in the scores of autistic children in both receptive and expressive language throughout the study (i.e., during the intervention period and in the 3-month period after the intervention). Standard scores suggested improvement only in the receptive language scale during the intervention period. Standard scores showed a floor effect for children who scored at −3 SD below the mean. Conclusions: Findings suggested that GSVs were not only psychometrically sound but also the most sensitive measure of direct changes in skills compared to raw, standard, and age-equivalent scores. Floor effects may limit the sensitivity of standard scores to detect changes in children’s skills. Strengths, limitations, and interpretations of each of the scoring approaches in measuring changes in skills during intervention were discussed. Supplemental Material S1. Effect size of changes from intervention as measured by each scoring approaches (with nonparametric Wilcoxon signed-rank test). Kwok, E., Feiner, H., Grauzer, J., Kaat, A., & Roberts, M. Y. (2022). Measuring change during intervention using norm-referenced, standardized measures: A comparison of raw scores, standard scores, age equivalents, and growth scale values from the Preschool Language Scales–Fifth Edition. Journal of Speech, Language, and Hearing Research. Advance online publication. https://doi.org/10.1044/2022_JSLHR-22-00122</p

Lagging spawning and increasing phenological extremes jeopardize walleye (Sander vitreus) in north‐temperate lakes

Abstract The phenology of critical biological events in aquatic ecosystems is rapidly shifting due to climate change. Growing variability in phenological cues can increase the likelihood of trophic mismatches (i.e., mismatches in the timing of peak prey and predator abundances), causing recruitment failures in important fisheries. We assessed changes in the spawning phenology of walleye (Sander vitreus) in 194 Midwest US lakes to investigate factors influencing walleye phenological responses to climate change and associated climate variability, including ice‐off timing, lake physical characteristics, and population stocking history. Ice‐off phenology shifted earlier, about three times faster than walleye spawning phenology over time. Spawning phenology deviations from historic averages increased in magnitude over time, and large deviations were associated with poor offspring survival. Our results foreshadow the risks of increasingly frequent natural recruitment failures due to mismatches between historically tightly coupled spawning and ice‐off phenology

Dynamic cerebral autoregulation in Alzheimer's disease and mild cognitive impairment: A systematic review.

Dynamic cerebral autoregulation (dCA) is a key mechanism that regulates cerebral blood flow (CBF) in response to transient changes in blood pressure (BP). Impairment of dCA could increase vulnerability to hypertensive vascular damage, but also to BP lowering effects of antihypertensive treatment. The literature remains conflicted on whether dCA is altered in Alzheimer's disease (AD) and mild cognitive impairment (MCI). We summarized available data on dCA in AD and MCI, by searching PubMed, Embase, PsycINFO and Web of Science databases (inception-January 2022). Eight studies (total n = 443) were included in the qualitative synthesis of which seven were eligible for meta-analysis. All studies used Transcranial Doppler (TCD) ultrasonography and transfer function analysis or the autoregulatory index to assess dCA during spontaneous or induced BP fluctuations. Meta-analysis indicated no significant difference between AD, MCI and healthy controls in dCA parameters for spontaneous fluctuations. For induced fluctuations, the available data were limited, but indicative of at least preserved and possibly better autoregulatory functioning in AD and MCI compared to controls. In summary, current evidence does not suggest poorer dCA efficiency in AD or MCI. Further work is needed to investigate dCA in dementia with induced fluctuations controlling for changes in end-tidal carbon dioxide.</p

Chromosome-scale genome assembly of the brown anole (Anolis sagrei), an emerging model species

Rapid technological improvements are democratizing access to high quality, chromosome-scale genome assemblies. No longer the domain of only the most highly studied model organisms, now non-traditional and emerging model species can be genome-enabled using a combination of sequencing technologies and assembly software. Consequently, old ideas built on sparse sampling across the tree of life have recently been amended in the face of genomic data drawn from a growing number of high-quality reference genomes. Arguably the most valuable are those long-studied species for which much is already known about their biology; what many term emerging model species. Here, we report a highly complete chromosome-scale genome assembly for the brown anole, Anolis sagrei – a lizard species widely studied across a variety of disciplines and for which a high-quality reference genome was long overdue. This assembly exceeds the vast majority of existing reptile and snake genomes in contiguity (N50 = 253.6 Mb) and annotation completeness. Through the analysis of this genome and population resequence data, we examine the history of repetitive element accumulation, identify the X chromosome, and propose a hypothesis for the evolutionary history of fusions between autosomes and the X that led to the sex chromosomes of A. sagrei

The African coelacanth genome provides insights into tetrapod evolution.

The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution