Demography reveals populational expansion of a recently extinct Iberian ungulate

Reconstructing the demographic history of endangered taxa is paramount to predict future fluctuations and disentangle the contributing factors. Extinct taxa or populations might also provide key insights in this respect by means of the DNA extracted from museum specimens. Nevertheless, the degraded status of biological material and the limited number of records may pose some constraints. For this reason, identifying all available sources, including private and public biological collections, is a crucial step forward. In this study, we reconstructed the demographic history based on cytochrome-b sequence data of the Pyrenean ibex (Capra pyrenaica pyrenaica), a charismatic taxon of the European wildlife that became extinct in the year 2000. Moreover, we built a database of the museum specimens available in public biological collections worldwide and genotyped a privately owned 140-year-old trophy from the Spanish Pyrenees to confirm its origin. We found that the population of the Pyrenean ibex underwent a recent expansion approximately 20,000 years ago, after which trophy hunting and epizootics triggered a relentless population decline. Our interpretations, based on the genetic information currently available in public repositories, provide a solid basis for more exhaustive analyses relying on all the new sources identified. In particular, the adoption of a genome-wide approach appears a fundamental prerequisite to disentangle the multiple contributing factors associated with low genetic diversity, including inbreeding depression, acting as extinction drivers.

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Extensive population decline in the Tasmanian devil predates European settlement and devil facial tumour disease

Biology Letters ◽

10.1098/rsbl.2014.0619 ◽

2014 ◽

Vol 10 (11) ◽

pp. 20140619 ◽

Cited By ~ 47

Author(s):

Anna Brüniche-Olsen ◽

Menna E. Jones ◽

Jeremy J. Austin ◽

Christopher P. Burridge ◽

Barbara R. Holland

Keyword(s):

Genetic Diversity ◽

Environmental Changes ◽

Southern Oscillation ◽

Demographic History ◽

Population Decline ◽

Tasmanian Devil ◽

Term Survival ◽

Temporal Sampling ◽

Low Genetic Diversity ◽

Devil Facial Tumour Disease

The Tasmanian devil ( Sarcophilus harrisii ) was widespread in Australia during the Late Pleistocene but is now endemic to the island of Tasmania. Low genetic diversity combined with the spread of devil facial tumour disease have raised concerns for the species’ long-term survival. Here, we investigate the origin of low genetic diversity by inferring the species' demographic history using temporal sampling with summary statistics, full-likelihood and approximate Bayesian computation methods. Our results show extensive population declines across Tasmania correlating with environmental changes around the last glacial maximum and following unstable climate related to increased ‘El Niño–Southern Oscillation’ activity.

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The demographic history of Madagascan micro-endemics: have rare species always been rare?

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2021.0957 ◽

2021 ◽

Vol 288 (1959) ◽

pp. 20210957

Author(s):

Andrew J. Helmstetter ◽

Stuart Cable ◽

Franck Rakotonasolo ◽

Romer Rabarijaona ◽

Mijoro Rakotoarinivo ◽

...

Keyword(s):

Plant Species ◽

Threatened Species ◽

Sequence Data ◽

Extinction Risk ◽

Demographic History ◽

Population Decline ◽

Rapid Decline ◽

Effective Population ◽

Conservation Assessment ◽

Data Deficient

Extinction has increased as human activities impact ecosystems, yet relatively few species have conservation assessments. Novel approaches are needed to highlight threatened species that are currently data-deficient. Many Madagascan plant species have extremely narrow ranges, but this may not have always been the case—it is unclear how the island's diverse flora evolved. To assess this, we generated restriction-site associated DNA sequence data for 10 Madagascan plant species, estimated effective population size ( N e ) for each species and compared this to census ( N c ) sizes. In each case, N e was an order of magnitude larger than N c —signifying rapid, recent population decline. We then estimated species' demographic history, tracking changes in N e over time. We show that it is possible to predict extinction risk, particularly in the most threatened species. Furthermore, simulations showed that our approach has the power to detect population decline during the Anthropocene. Our analyses reveal that Madagascar's micro-endemics were not always rare, having experienced a rapid decline in their recent history. This casts further uncertainty over the processes that generated Madagascar's exceptional biodiversity. Our approach targets data-deficient species in need of conservation assessment, particularly in regions where human modification of the environment has been rapid.

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An Integrated Framework for the Inference of Viral Population History From Reconstructed Genealogies

Genetics ◽

10.1093/genetics/155.3.1429 ◽

2000 ◽

Vol 155 (3) ◽

pp. 1429-1437

Author(s):

Oliver G Pybus ◽

Andrew Rambaut ◽

Paul H Harvey

Keyword(s):

Maximum Likelihood ◽

Sequence Data ◽

Demographic History ◽

Population History ◽

Maximum Likelihood Estimates ◽

Viral Population ◽

True Parameter ◽

Subtype B ◽

Exponential Growth Model ◽

Parameter Values

Abstract We describe a unified set of methods for the inference of demographic history using genealogies reconstructed from gene sequence data. We introduce the skyline plot, a graphical, nonparametric estimate of demographic history. We discuss both maximum-likelihood parameter estimation and demographic hypothesis testing. Simulations are carried out to investigate the statistical properties of maximum-likelihood estimates of demographic parameters. The simulations reveal that (i) the performance of exponential growth model estimates is determined by a simple function of the true parameter values and (ii) under some conditions, estimates from reconstructed trees perform as well as estimates from perfect trees. We apply our methods to HIV-1 sequence data and find strong evidence that subtypes A and B have different demographic histories. We also provide the first (albeit tentative) genetic evidence for a recent decrease in the growth rate of subtype B.

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De Novo Genome Assembly of Limpet Bathyacmaea lactea (Gastropoda: Pectinodontidae): The First Reference Genome of a Deep-Sea Gastropod Endemic to Cold Seeps

Genome Biology and Evolution ◽

10.1093/gbe/evaa100 ◽

2020 ◽

Vol 12 (6) ◽

pp. 905-910 ◽

Cited By ~ 2

Author(s):

Ruoyu Liu ◽

Kun Wang ◽

Jun Liu ◽

Wenjie Xu ◽

Yang Zhou ◽

...

Keyword(s):

Deep Sea ◽

Metal Ion ◽

De Novo ◽

Demographic History ◽

Gene Families ◽

Phylogenetic Position ◽

Cold Seeps ◽

Nitrogen And Phosphorus ◽

De Novo Genome Assembly ◽

A Genome

Abstract Cold seeps, characterized by the methane, hydrogen sulfide, and other hydrocarbon chemicals, foster one of the most widespread chemosynthetic ecosystems in deep sea that are densely populated by specialized benthos. However, scarce genomic resources severely limit our knowledge about the origin and adaptation of life in this unique ecosystem. Here, we present a genome of a deep-sea limpet Bathyacmaea lactea, a common species associated with the dominant mussel beds in cold seeps. We yielded 54.6 gigabases (Gb) of Nanopore reads and 77.9-Gb BGI-seq raw reads, respectively. Assembly harvested a 754.3-Mb genome for B. lactea, with 3,720 contigs and a contig N50 of 1.57 Mb, covering 94.3% of metazoan Benchmarking Universal Single-Copy Orthologs. In total, 23,574 protein-coding genes and 463.4 Mb of repetitive elements were identified. We analyzed the phylogenetic position, substitution rate, demographic history, and TE activity of B. lactea. We also identified 80 expanded gene families and 87 rapidly evolving Gene Ontology categories in the B. lactea genome. Many of these genes were associated with heterocyclic compound metabolism, membrane-bounded organelle, metal ion binding, and nitrogen and phosphorus metabolism. The high-quality assembly and in-depth characterization suggest the B. lactea genome will serve as an essential resource for understanding the origin and adaptation of life in the cold seeps.

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Comparing maternal genetic variation across two millennia reveals the demographic history of an ancient human population in southwest Turkey

Royal Society Open Science ◽

10.1098/rsos.150250 ◽

2016 ◽

Vol 3 (2) ◽

pp. 150250 ◽

Cited By ~ 9

Author(s):

Claudio Ottoni ◽

Rita Rasteiro ◽

Rinse Willet ◽

Johan Claeys ◽

Peter Talloen ◽

...

Keyword(s):

Demographic History ◽

Population Decline ◽

Fifth Century ◽

Seventh Century ◽

Human Occupation ◽

Dna Variation ◽

Genetic Discontinuity ◽

History Of ◽

The City ◽

Modern Sample

More than two decades of archaeological research at the site of Sagalassos, in southwest Turkey, resulted in the study of the former urban settlement in all its features. Originally settled in late Classical/early Hellenistic times, possibly from the later fifth century BCE onwards, the city of Sagalassos and its surrounding territory saw empires come and go. The Plague of Justinian in the sixth century CE, which is considered to have caused the death of up to a third of the population in Anatolia, and an earthquake in the seventh century CE, which is attested to have devastated many monuments in the city, may have severely affected the contemporary Sagalassos community. Human occupation continued, however, and Byzantine Sagalassos was eventually abandoned around 1200 CE. In order to investigate whether these historical events resulted in demographic changes across time, we compared the mitochondrial DNA variation of two population samples from Sagalassos (Roman and Middle Byzantine) and a modern sample from the nearby town of Ağlasun. Our analyses revealed no genetic discontinuity across two millennia in the region and Bayesian coalescence-based simulations indicated that a major population decline in the area coincided with the final abandonment of Sagalassos, rather than with the Plague of Justinian or the mentioned earthquake.

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Nucleotide sequences of highly repeated DNAs; compilation and comments

Genetics Research ◽

10.1017/s0016672300020711 ◽

1982 ◽

Vol 39 (1) ◽

pp. 1-30 ◽

Cited By ~ 33

Author(s):

George L. Gabor Miklos ◽

Amanda Clare Gill

Keyword(s):

Satellite Dna ◽

Germ Line ◽

Sequence Data ◽

Allelic Variation ◽

Neutral Theory ◽

Natural Populations ◽

Evolutionary Significance ◽

Nucleotide Sequence Data ◽

A Genome ◽

Repeated Dnas

SummaryThe nucleotide sequence data from highly repeated DNAs of inverte-brates and mammals are summarized and briefly discussed. Very similar conclusions can be drawn from the two data bases. Sequence complexities can vary from 2 bp to at least 359 bp in invertebrates and from 3 bp to at least 2350 bp in mammals. The larger sequences may or may not exhibit a substructure. Significant sequence variation occurs for any given repeated array within a species, but the sources of this heterogeneity have not been systematically partitioned. The types of alterations in a basic repeating unit can involve base changes as well as deletions or additions which can vary from 1 bp to at least 98 bp in length. These changes indicate that sequence per se is unlikely to be under significant biological constraints and may sensibly be examined by analogy to Kimura's neutral theory for allelic variation. It is not possible with the present evidence to discriminate between the roles of neutral and selective mechanisms in the evolution of highly repeated DNA.Tandemly repeated arrays are constantly subjected to cycles of amplification and deletion by mechanisms for which the available data stem largely from ribosomal genes. It is a matter of conjecture whether the solutions to the mechanistic puzzles involved in amplification or rapid redeployment of satellite sequences throughout a genome will necessarily give any insight into biological functions.The lack of significant somatic effects when the satellite DNA content of a genome is significantly perturbed indicates that the hunt for specific functions at the cellular level is unlikely to prove profitable.The presence or in some cases the amount of satellite DNA on a chromosome, however, can have significant effects in the germ line. There the data show that localized condensed chromatin, rich in satellite DNA, can have the effect of rendering adjacent euchromatic regions rec−, or of altering levels of recombination on different chromosomes. No data stemming from natural populations however are yet available to tell us if these effects are of adaptive or evolutionary significance.

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Transcriptome analysis ofSchistosoma mansonilarval development using serial analysis of gene expression (SAGE)

Parasitology ◽

10.1017/s0031182009005733 ◽

2009 ◽

Vol 136 (5) ◽

pp. 469-485 ◽

Cited By ~ 22

Author(s):

A. S. TAFT ◽

J. J. VERMEIRE ◽

J. BERNIER ◽

S. R. BIRKELAND ◽

M. J. CIPRIANO ◽

...

Keyword(s):

Gene Expression ◽

Sequence Data ◽

Subsequent Development ◽

Differentially Expressed ◽

Cdna Libraries ◽

Genome Wide ◽

A Genome ◽

Genome Wide Expression ◽

Cell Conditioned Medium

SUMMARYInfection of the snail,Biomphalaria glabrata, by the free-swimming miracidial stage of the human blood fluke,Schistosoma mansoni, and its subsequent development to the parasitic sporocyst stage is critical to establishment of viable infections and continued human transmission. We performed a genome-wide expression analysis of theS. mansonimiracidia and developing sporocyst using Long Serial Analysis of Gene Expression (LongSAGE). Five cDNA libraries were constructed from miracidia andin vitrocultured 6- and 20-day-old sporocysts maintained in sporocyst medium (SM) or in SM conditioned by previous cultivation with cells of theB. glabrataembryonic (Bge) cell line. We generated 21 440 SAGE tags and mapped 13 381 to theS. mansonigene predictions (v4.0e) either by estimating theoretical 3′ UTR lengths or using existing 3′ EST sequence data. Overall, 432 transcripts were found to be differentially expressed amongst all 5 libraries. In total, 172 tags were differentially expressed between miracidia and 6-day conditioned sporocysts and 152 were differentially expressed between miracidia and 6-day unconditioned sporocysts. In addition, 53 and 45 tags, respectively, were differentially expressed in 6-day and 20-day cultured sporocysts, due to the effects of exposure to Bge cell-conditioned medium.

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Reef development and Sea level changes drive Acanthaster Population Expansion in the Indo-Pacific region

10.1101/2020.11.18.388207 ◽

2020 ◽

Author(s):

P.C. Pretorius ◽

T.B. Hoareau

Keyword(s):

Population Size ◽

Sea Level ◽

Environmental Changes ◽

Sequence Data ◽

Demographic History ◽

Population Expansion ◽

Population Level ◽

Sea Level Changes ◽

Reef Development ◽

Curve Fitting Method

AbstractMolecular clock calibration is central in population genetics as it provides an accurate inference of demographic history, whereby helping with the identification of driving factors of population changes in an ecosystem. This is particularly important for coral reef species that are seriously threatened globally and in need of conservation. Biogeographic events and fossils are the main source of calibration, but these are known to overestimate timing and parameters at population level, which leads to a disconnection between environmental changes and inferred reconstructions. Here, we propose the Last Glacial Maximum (LGM) calibration that is based on the assumptions that reef species went through a bottleneck during the LGM, which was followed by an early yet marginal increase in population size. We validated the LGM calibration using simulations and genetic inferences based on Extended Bayesian Skyline Plots. Applying it to mitochondrial sequence data of crown-of-thorns starfish Acanthaster spp., we obtained mutation rates that were higher than phylogenetically based calibrations and varied among populations. The timing of the greatest increase in population size differed slightly among populations, but all started between 10 and 20 kya. Using a curve-fitting method, we showed that Acanthaster populations were more influenced by sea-level changes in the Indian Ocean and by reef development in the Pacific Ocean. Our results illustrate that the LGM calibration is robust and can probably provide accurate demographic inferences in many reef species. Application of this calibration has the potential to help identify population drivers that are central for the conservation and management of these threatened ecosystems.

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Deep learning predicts short non-coding RNA functions from only raw sequence data

PLoS Computational Biology ◽

10.1371/journal.pcbi.1008415 ◽

2020 ◽

Vol 16 (11) ◽

pp. e1008415

Author(s):

Teresa Maria Rosaria Noviello ◽

Francesco Ceccarelli ◽

Michele Ceccarelli ◽

Luigi Cerulo

Keyword(s):

Secondary Structure ◽

Sequence Data ◽

Computational Cost ◽

Large Data ◽

Sequence Information ◽

Structure Information ◽

Non Coding Rna ◽

A Genome ◽

Data Volume ◽

Biological Functionality

Small non-coding RNAs (ncRNAs) are short non-coding sequences involved in gene regulation in many biological processes and diseases. The lack of a complete comprehension of their biological functionality, especially in a genome-wide scenario, has demanded new computational approaches to annotate their roles. It is widely known that secondary structure is determinant to know RNA function and machine learning based approaches have been successfully proven to predict RNA function from secondary structure information. Here we show that RNA function can be predicted with good accuracy from a lightweight representation of sequence information without the necessity of computing secondary structure features which is computationally expensive. This finding appears to go against the dogma of secondary structure being a key determinant of function in RNA. Compared to recent secondary structure based methods, the proposed solution is more robust to sequence boundary noise and reduces drastically the computational cost allowing for large data volume annotations. Scripts and datasets to reproduce the results of experiments proposed in this study are available at: https://github.com/bioinformatics-sannio/ncrna-deep.

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Limits and Convergence properties of the Sequentially Markovian Coalescent

10.1101/2020.07.23.217091 ◽

2020 ◽

Author(s):

Thibaut Sellinger ◽

Diala Abu Awad ◽

Aurélien Tellier

Keyword(s):

Sequence Data ◽

Demographic History ◽

Simulated Data ◽

Simultaneous Estimation ◽

Data Sets ◽

Performance Limits ◽

Biological Variables ◽

Convergence Proofs ◽

New Interpretation ◽

Population Demographic

AbstractMany methods based on the Sequentially Markovian Coalescent (SMC) have been and are being developed. These methods make use of genome sequence data to uncover population demographic history. More recently, new methods have extended the original theoretical framework, allowing the simultaneous estimation of the demographic history and other biological variables. These methods can be applied to many different species, under different model assumptions, in hopes of unlocking the population/species evolutionary history. Although convergence proofs in particular cases have been given using simulated data, a clear outline of the performance limits of these methods is lacking. We here explore the limits of this methodology, as well as present a tool that can be used to help users quantify what information can be confidently retrieved from given datasets. In addition, we study the consequences for inference accuracy violating the hypotheses and the assumptions of SMC approaches, such as the presence of transposable elements, variable recombination and mutation rates along the sequence and SNP call errors. We also provide a new interpretation of the SMC through the use of the estimated transition matrix and offer recommendations for the most efficient use of these methods under budget constraints, notably through the building of data sets that would be better adapted for the biological question at hand.

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