scholarly journals Reference genome and demographic history of the most endangered marine mammal, the vaquita

2020 ◽  
Author(s):  
Phillip A. Morin ◽  
Frederick I. Archer ◽  
Catherine D. Avila ◽  
Jennifer R. Balacco ◽  
Yury V. Bukhman ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Marine Mammal ◽  
Reference Genome ◽  
Demographic History ◽  
Mammalian Species ◽  
Small Population ◽  
Chromosome Length ◽  
Rapid Decline ◽  
History Of

AbstractThe vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline resulting from inadvertent deaths due to the increasing use of large-mesh gillnets for more than 20 years. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome-length autosome scaffolds and the X-chromosome scaffold, with a scaffold N50 of 115 Mb. Genome-wide heterozygosity is the lowest (0.01%) of any mammalian species analyzed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long-term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long-term population stability at less than 5000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.

scholarly journals Reference genome and demographic history of the most endangered marine mammal, the vaquita

2020 ◽  
Author(s):  
Phillip A. Morin ◽  
Frederick I. Archer ◽  
Catherine D. Avila ◽  
Jennifer R. Balacco ◽  
Yury V. Bukhman ◽  
...  
Keyword(s):  
Marine Mammal ◽  
Reference Genome ◽  
Demographic History ◽  
History Of

scholarly journals One Step Away From Extinction: A Population Genomic Analysis of A Narrow Endemic, Tropical Plant Species

2021 ◽  
Vol 12 ◽  
Author(s):  
Thais M. Teixeira ◽  
Alison G. Nazareno
Keyword(s):  
Genetic Diversity ◽  
Missing Data ◽  
Plant Species ◽  
Threatened Species ◽  
Demographic History ◽  
Small Population ◽  
Narrow Endemic ◽  
Population Genomic ◽  
Genomic Study ◽  
History Of

Intraspecific genetic variation plays a fundamental role in maintaining the evolutionary potential of wild populations. Hence, the assessment of genetic diversity patterns becomes essential to guide biodiversity conservation policies, particularly for threatened species. To inform management strategies for conservation of Mimosa catharinensis – a narrow endemic, critically endangered plant species – we identified 1,497 unlinked SNP markers derived from a reduced representation sequencing method (i.e., double digest restriction site associated DNA sequencing, or ddRADseq). This set of molecular markers was employed to assess intrapopulation genetic parameters and the demographic history of one extremely small population of M. catharinensis (N=33) located in the Brazilian Atlantic Forest. Contrary to what is expected for narrow endemic and threatened species with small population sizes, we observed a moderate level of genetic diversity for M. catharinensis [uHE(0%missing data)=0.205, 95% CI (0.160, 0.250); uHE(30%missing data)=0.233, 95% CI (0.174, 0.292)]. Interestingly, M. catharinensis, which is a lianescent shrub with no indication of seed production for at least two decades, presented high levels of outcrossing [t(0%missing data)=0.883, SE±0.0483; t(30%missing data)=0.909, SE±0.011] and an apparent absence of inbreeding [F(0%missing data)=−0.145, 95% CI (−0.189, −0.101); F(30%missing data)=−0.105, 95% CI (−0.199, −0.011)]. However, the reconstruction of demographic history of M. catharinensis indicated that the population should be suffered a recent bottleneck. Our population genomic study tackles a central issue in evolution and conservation biology and we expect that it will be useful to help safeguard the remaining genetic diversity reported for this unique genetic resource.

A Minimal Demographic History of Israel

2019 ◽  
Author(s):  
Sergio DellaPergola
Keyword(s):  
Socioeconomic Development ◽  
Large Scale ◽  
Population Change ◽  
Demographic History ◽  
Mass Movement ◽  
Jewish People ◽  
Population Projections ◽  
Demographic Development ◽  
History Of

This chapter surveys the demographic development of Israel/Palestine from antiquity through the present and looking toward the future. Territory and habitability is described regarding changing boundary definitions and internal divisions that have reflected shifting political rule. Population change is examined in the long term, noting the significant historical ups and downs in population size and socioeconomic development. The development of contemporary population in Israel and Palestine reflects large-scale international migration, including mass movement of Jewish and Arab refugees. Variable fertility levels and birth rates have also significantly affected the pace of population growth. Attention is paid to the more recent balance of Jews and Palestinians over the whole territory between the Mediterranean Sea and the Jordan River, and an overview is presented of the distribution of world Jewish and Palestinian diasporas. Finally, population projections for the Jewish people, the state of Israel, and the whole territory of Israel/Palestine are presented.

scholarly journals Long-term natural history of visual acuity in eyes with choroideremia: a systematic review and meta-analysis of data from 1004 individual eyes

2020 ◽  
pp. bjophthalmol-2020-316028
Author(s):  
Liangbo L Shen ◽  
Aneesha Ahluwalia ◽  
Mengyuan Sun ◽  
Benjamin K Young ◽  
Holly K Grossetta Nardini ◽  
...  
Keyword(s):  
Visual Acuity ◽  
Natural History ◽  
Primary Endpoint ◽  
Meta Analysis ◽  
Young Patients ◽  
Rapid Decline ◽  
Transition Age ◽  
Individual Level ◽  
History Of

Background/aimsBest-corrected visual acuity (BCVA) is the most common primary endpoint in treatment trials for choroideremia (CHM) but the long-term natural history of BCVA is unclear.MethodsWe searched in seven databases to identify studies that reported BCVA of untreated eyes with CHM. We sought individual-level data and performed segmented regression between BCVA and age. For eyes followed longitudinally, we introduced a horizontal translation factor to each dataset to account for different ages at onset of a rapid BCVA decline.ResultsWe included 1004 eyes from 23 studies. BCVA of the right and left eyes was moderately correlated (r=0.60). BCVA as a function of age followed a 2-phase decline (slow followed by rapid decline), with an estimated transition age of 39.1 years (95% CI 33.5 to 44.7). After the introduction of horizontal translation factors to longitudinal datasets, BCVA followed a 2-phase decline until it reached 0 letters (r2=0.90). The BCVA decline rate was 0.33 letters/year (95% CI −0.38 to 1.05) before 39 years, and 1.23 letters/year (95% CI 0.55 to 1.92) after 39 years (p=0.004).ConclusionBCVA in eyes with CHM follows a 2-phase linear decline with a transition age of approximately 39 years. Future trials enrolling young patients may not be able to use BCVA as a primary or sole endpoint, but rather, may need to employ additional disease biomarkers that change before age 39. BCVA may still have utility as a primary endpoint for patients older than 39 years who have measurable BCVA decline rates.

scholarly journals Distribution, Diversity, and Evolution of Endogenous Retroviruses in Perissodactyl Genomes

2018 ◽  
Vol 92 (23) ◽  
Author(s):  
Henan Zhu ◽  
Robert James Gifford ◽  
Pablo Ramiro Murcia
Keyword(s):  
Germ Line ◽  
Mammalian Species ◽  
Endogenous Retroviruses ◽  
Functional Roles ◽  
Physiological Processes ◽  
Great Utility ◽  
White Rhinoceros ◽  
History Of ◽  
Mammalian Genomes

ABSTRACTThe evolution of mammalian genomes has been shaped by interactions with endogenous retroviruses (ERVs). In this study, we investigated the distribution and diversity of ERVs in the mammalian orderPerissodactyla, with a view to understanding their impact on the evolution of modern equids (familyEquidae). We characterize the major ERV lineages in the horse genome in terms of their genomic distribution, ancestral genome organization, and time of activity. Our results show that subsequent to their ancestral divergence from rhinoceroses and tapirs, equids acquired four novel ERV lineages. We show that two of these ERV lineages proliferated extensively in the lineage leading to modern horses, and one contains loci that are actively transcribed in specific tissues. In addition, we show that the white rhinoceros has resisted germ line colonization by retroviruses for more than 54 million years—longer than any other extant mammalian species. The map of equine ERVs that we provide here will be of great utility to future studies aiming to investigate the potential functional roles of equine ERVs and their impact on equine evolution.IMPORTANCEERVs in the host genome are highly informative about the long-term interactions of retroviruses and hosts. They are also interesting because they have influenced the evolution of mammalian genomes in various ways. In this study, we derive a calibrated timeline describing the process through which ERV diversity has been generated in the equine germ line. We determined the distribution and diversity of perissodactyl ERV lineages and inferred their retrotranspositional activity during evolution, thereby gaining insight into the long-term coevolutionary history of retroviruses and mammals. Our study provides a platform for future investigations to identify equine ERV loci involved in physiological processes and/or pathological conditions.

scholarly journals Chromosome-level reference genome of the jellyfish Rhopilema esculentum

GigaScience ◽  
2020 ◽  
Vol 9 (4) ◽  
Author(s):  
Yunfeng Li ◽  
Lei Gao ◽  
Yongjia Pan ◽  
Meilin Tian ◽  
Yulong Li ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Evolutionary History ◽  
Reference Genome ◽  
Protein Coding ◽  
Fishery Resource ◽  
Rhopilema Esculentum ◽  
Sequencing Technologies ◽  
Genome Wide ◽  
History Of ◽  
Chromosome Level

Abstract Background Jellyfish belong to the phylum Cnidaria, which occupies an important phylogenetic location in the early-branching Metazoa lineages. The jellyfish Rhopilema esculentum is an important fishery resource in China. However, the genome resource of R. esculentum has not been reported to date. Findings In this study, we constructed a chromosome-level genome assembly of R. esculentum using Pacific Biosciences, Illumina, and Hi-C sequencing technologies. The final genome assembly was ∼275.42 Mb, with a contig N50 length of 1.13 Mb. Using Hi-C technology to identify the contacts among contigs, 260.17 Mb (94.46%) of the assembled genome were anchored onto 21 pseudochromosomes with a scaffold N50 of 12.97 Mb. We identified 17,219 protein-coding genes, with an average CDS length of 1,575 bp. The genome-wide phylogenetic analysis indicated that R. esculentum might have evolved more slowly than the other scyphozoan species used in this study. In addition, 127 toxin-like genes were identified, and 1 toxin-related “hub” was found by a genomic survey. Conclusions We have generated a chromosome-level genome assembly of R. esculentum that could provide a valuable genomic background for studying the biology and pharmacology of jellyfish, as well as the evolutionary history of Cnidaria.

scholarly journals Childhood epidemics and the demographic landscape of the Aland Archipelago

2018 ◽  
Author(s):  
◽  
Erin Lee Miller
Keyword(s):  
Immune Suppression ◽  
Excess Mortality ◽  
Demographic History ◽  
Childhood Diseases ◽  
Secondary Infections ◽  
Epidemic Period ◽  
History Of ◽  
Susceptible Populations ◽  
Expected Mortality

Historically, the introduction of childhood diseases such as measles or smallpox resulted in the infection of nearly every susceptible individual in a community. While smallpox has long been considered the deadlier of the two childhood diseases, research has shown that the immune response to measles infection results in immune suppression that can last for weeks or even months. Higher mortality during measles epidemics has typically been associated with completely susceptible populations; however, in Aland, Finland--a population that experienced regular epidemics of both childhood diseases--mortality from all causes during the 1820-21 measles epidemic was 25% higher than that experienced during the 1823-24 smallpox epidemic. Excess mortality surrounding measles epidemics suggests that this disease may have larger impacts on the demographic history of populations than previously thought. This study uses archival records to investigate syndemic interactions between measles and other diseases during a 19th century measles epidemic in the Aland Islands, Finland. Comparisons to smallpox and a non-epidemic period indicated greater than expected mortality for individuals aged 5 to 9 years and over 50 years; though neither epidemic had long-term demographic consequences. These results are consistent with deaths from secondary infections due to measles-induced immune suppression, but not conclusive. The unknown impact of measles exposure on adults with antibodies, and the variety of other diseases and symptom descriptions, indicates that the possibility of co-occurring epidemics cannot be ruled out.

Introduction

Animal Ethos ◽  
2018 ◽  
pp. 1-32
Author(s):  
Lesley A. Sharp
Keyword(s):  
Science And Technology Studies ◽  
Animal Studies ◽  
Mammalian Species ◽  
The United States ◽  
Social Worlds ◽  
Important Distinction ◽  
Ethical Frameworks ◽  
History Of ◽  
Interspecies Encounters

The moral entanglements of human-animal relations have complex histories, as evidenced in anthropology’s longstanding interest in the relevance of interspecies encounters in shaping social worlds. This chapter begins with a history of my ethnographic project. I then discuss the long-term anthropological engagement with moral systems and the disciplinary relevance of the term ethos, where quotidian thought and action are central anthropological concerns. Ethos offers a potent approach to the study of science, where regulatory ethical frameworks overshadow the everyday and ordinary. I clarify the book’s terminology, with an important distinction between ethics (codified bioethical principles) and the unscripted, personal moral responses that animals inspire in the humans who work with them. Different animals inspire different moral responses; mammalian species are especially affectively potent, and certain kinds of animals (rats, dogs, monkeys) enable me to track different sorts of moral responses among lab personnel. As a result, certain kinds of animals will figure as a means to foreground particular themes and sentiments. I situate this work within the context of animal studies and science and technology studies, and I track the history of animal welfare and activism, especially in the United States and United Kingdom. The chapter concludes with an overview of my study. I also explain the relevance of the book’s three overarching sections, “Intimacy,” “Sacrifice,” and “Exceptionalism.”

scholarly journals Retroviruses drive the rapid evolution of mammalianAPOBEC3genes

2019 ◽  
Vol 117 (1) ◽  
pp. 610-618 ◽  
Author(s):  
Jumpei Ito ◽  
Robert J. Gifford ◽  
Kei Sato
Keyword(s):  
Gene Family ◽  
Fossil Record ◽  
Driving Force ◽  
Mammalian Species ◽  
Rapid Evolution ◽  
Endogenous Retroviruses ◽  
Mammalian Evolution ◽  
History Of ◽  
Mammalian Genomes

APOBEC3(A3) genes are members of theAID/APOBECgene family that are found exclusively in mammals.A3genes encode antiviral proteins that restrict the replication of retroviruses by inducing G-to-A mutations in their genomes and have undergone extensive amplification and diversification during mammalian evolution. Endogenous retroviruses (ERVs) are sequences derived from ancient retroviruses that are widespread mammalian genomes. In this study we characterize theA3repertoire and use the ERV fossil record to explore the long-term history of coevolutionary interaction between A3s and retroviruses. We examine the genomes of 160 mammalian species and identify 1,420AID/APOBEC-related genes, including representatives of previously uncharacterized lineages. We show thatA3genes have been amplified in mammals and that amplification is positively correlated with the extent of germline colonization by ERVs. Moreover, we demonstrate that the signatures of A3-mediated mutation can be detected in ERVs found throughout mammalian genomes and show that in mammalian species with expandedA3repertoires, ERVs are significantly enriched for G-to-A mutations. Finally, we show thatA3amplification occurred concurrently with prominent ERV invasions in primates. Our findings establish that conflict with retroviruses is a major driving force for the rapid evolution of mammalianA3genes.

scholarly journals The Demographic History of Micro-endemics: Have Rare Species Always Been Rare?

2020 ◽  
Author(s):  
Andrew J. Helmstetter ◽  
Stuart Cable ◽  
Franck Rakotonasolo ◽  
Romer Rabarijaona ◽  
Mijoro Rakotoarinivo ◽  
...  
Keyword(s):  
Threatened Species ◽  
Rare Species ◽  
Extinction Risk ◽  
Demographic History ◽  
Population Decline ◽  
Rapid Decline ◽  
Conservation Assessment ◽  
History Of ◽  
Narrow Endemics ◽  
Data Deficient

AbstractExtinction has increased as human activities impact ecosystems. Conservation assessments for the IUCN red list are a fundamental tool in aiding the prevention of further extinction, yet, relatively few species have been thoroughly assessed. To increase the efficiency of assessments, novel approaches are needed to highlight threatened species that are currently data deficient. Many Madagascan plant species currently have extremely narrow ranges, but this may not have always been the case. To assess this, we used high-throughput DNA sequencing for 2-5 individuals of each species - reflecting the paucity of samples available for rare species. We estimated effective population size (Ne) for each species and compared this to census population (Nc) sizes when known. In each case, Ne was an order of magnitude larger than Nc – a signature of rapid, recent population decline. We then estimated the demographic history of each species, tracking changes in Ne over time. Five out of ten species displayed significant population declines towards the present (68–90% decreases). Our results for palm trees indicate that it is possible to predict extinction risk, particularly in the most threatened species. We performed simulations to show that our approach has the power to detect population decline during the Anthropocene, but performs less well when less data is used. Similar declines to those in palms were observed in data deficient species or those assessed as of least concern. These analyses reveal that Madagascar’s narrow endemics were not always rare, having experienced rapid decline in their recent history. Our approach offers the opportunity to target species in need of conservation assessment with little prior information, particularly in regions where human modification of the environment has been rapid.SummaryCurrent IUCN conservation assessment methods are reliant on observed declines in species population and range sizes over the last one hundred years, but for the majority of species this information is not available. We used a population genetic approach to reveal historical demographic decline in the rare endemic flora of Madagascar. These results show that it is possible to predict extinction risk from demographic patterns inferred from genetic data and that destructive human influence is likely to have resulted in the very high frequency of narrow endemics present on the island. Our approach will act as an important tool for rapidly assessing the threatened status of poorly known species in need of further study and conservation, particularly for tropical flora and fauna.

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