Historical Connectivity and Demography of the Ferocious Reef Crab, Eriphia ferox (Crustacea; Eriphiidae), Demonstrate That Taoyuan Algal Reef Is an Essential Population Source Along the East Taiwan Strait

The east Taiwan Strait is largely fringed by sandy and muddy habitats. However, a massive algal reef made of crustose coralline algae has been found along the coast off Taoyuan city in northwestern Taiwan. The porous structure of Taoyuan Algal Reef harbors high abundance and diversity in marine organisms, including the ferocious reef crab, Eriphia ferox. Such a pivotal geographic location and unique ecological features make Taoyuan Algal Reef a potential stepping stone connecting biotic reefs in the east Taiwan Strait, South China Sea to the south, and even the high latitude of Japan to the north. In this study, we examined the population connectivity and historical demography of E. ferox by analyzing mitochondrial cytochrome oxidase I (COI) fragments of 317 individuals sampled from 21 localities in the northwestern Pacific. Our analyses of haplotype network and pairwise FST comparisons revealed a lack of phylogeographical structure among E. ferox populations, implying the existence of a migration corridor connecting the South and East China Seas through the east Taiwan Strait. Multiple lines of evidence, including significant values in neutrality tests, unimodally shaped mismatch distributions, and Bayesian skyline plots elucidated the rapid population growth of E. ferox following the sea-level rise after Last Glacial Maximum (ca. 2–10 Ka). Such demographic expansion in E. ferox coincided with the time when Taoyuan Algal Reef started to build up around 7,500 years ago. Coalescent migration analyses further indicated that the large and continuous E. ferox population exclusively found in Datan Algal Reef, the heart of Taoyuan Algal Reef, was a source population exporting migrants both northward and southward to the adjacent populations. The bidirectional gene flow should be attributed to larval dispersal by ocean currents and secondary contact due to historical population expansion. Instead of serving as a stepping stone, our results support that Taoyuan Algal Reef is an essential population source for biotic reef-associated species along the east Taiwan Strait, and highlight the importance of conserving such a unique ecosystem currently threatened by anthropogenic development.

The distribution and conservation status of Tapirus terrestris in the South American Atlantic Forest

Tapirus terrestris is the largest South American land mammal, with an extensive historical distribution and capable of occupying diverse habitats, and yet its populations have declined across its range. In order to provide baseline data on the conservation status of tapirs in the Atlantic Forest, we conducted a long-term study in one landscape, visited 93 forests, and received 217 expert reports over the 15-year study. We estimate that 2,665–15,992 tapirs remain in 48 confirmed populations, occupying 26,654 km2 of forest or 1.78% of its original range in the biome. Historically, hunting and deforestation were the main causes of decline, but today population isolation is the principal long-term threat. Vortex models indicate that 31.3–68.8% and 70.8–93.8% of the populations are demographically and genetically non-viable over the next 100 years, respectively, and that only 3–14 populations are viable when considering both variables. Habitat use data indicate that tapirs are adaptable to disturbed and secondary forests and will use diverse tree plantations and agricultural lands but hunting and highways keep populations isolated. Reserve staff report tapirs as common/abundant at 62.2% of the sites, and populations as stable and growing in 60% and 36% of the sites, respectively, and there is ample habitat in the biome for a population expansion, but overcoming the causes of isolation will be necessary for this to occur. Lack of adequate funding for protecting reserves is a chronic threat throughout the biome, especially in federal and state/provincial reserves, and increased funding will be necessary to implement effective conservation plans.

Population Genetic Structure of Neoschoengastia Gallinarum in China Based on Mitochondrial DNA Markers

Background: Neoschoengastia gallinarum is a widespread agricultural pest in China.The larvae of N. gallinarum are parasitic on the body surface of poultry. Performance, carcass quality, and normal marketing of mite infected broilers are severely affected by pruritus and pockmark lesions on the body surface. In China, N. gallinarum research has primarily focused on occurrence regularity, biology, and control methods. The genetic structure, variation, and genetic relationship between the N. gallinarum populations in China are still unclear.Methods: Genetic variations and structure among populations of N. gallinarum was examined and analyzed based on the nucleotide sequences of a 1522 nt variable region of the mitochondrial tandem genes (COI, COII, and ND5) among 4 populations from 7 collection sites in southern China.Results: A total of 192 individuals in 4 populations were analyzed. The tandem genes sequences were aligned, and 75 haplotypes were detected, 4 of these shared between populations. The range of haplotype diversity was from 0.860 (FJ) to 0.978 (GX). The pairwise FST values among populations were higher (0.096-0.551).The haplotype network mediation map and phylogenetic tree showed that the haplotypes were divided into two clade, Which did not completely follow the distribution rule of geographical populations. The AMOVA result showed that the percentage of variation within populations (72.94%) was higher than that among populations (27.06%). Neutral test and mismatch analysisrevealed that N. gallinarum had not experienced an obvious population expansion in recent historical periods, and the population size was relatively stable.Conclusions: The N. gallinarum population showed high genetic diversity based on mitochondrial tandem genes analysis and strong ecological adaptability. Despite the fact that geogrphic isolation causes certain genetic differentiation among populations, N. gallinarum high gene flow among populations as a result of human trade activities, and there was no obvious geographical genetic structure.

The Role of Crop Protection in Sustainable Potato (Solanum tuberosum L.) Production to Alleviate Global Starvation Problem: An Overview

Among food crops in terms of consumption, potato ranks fourth, most important and valuable crop worldwide in terms of production and area harvested after maize, wheat and rice. In the coming years, potato production must keep pace with global population expansion nutritiously and sustainably which can partially be achieved by reducing the yield losses caused by the destructive pest and disease activities to the crop. The challenge of 70–80% total microbial crop yield loss posed by pathogens must be addressed for sustainable potato production in order to properly alleviate the global starvation problem. Potato as a food security crop can help to achieve the four food security requirements: food availability, quality, accessibility and stability. Health benefits of potato have shown the presence of phytochemicals as well as resistant starch which serve as anticancer and antidiabetic. The role of potato in the global food security should not be over emphasized, hence in this chapter we want to give an overview on the global hunger and food security at present, and the role played by potato as a food security crop. In addition, potato yield losses caused by pests and diseases especially phytopathogens, their etiology and the role of crop protection in sustainable potato production to alleviate global starvation problem will be discussed.

The provincial trend of population aging in China – based on population expansion forecast formula

China is one of the countries that have entered the stage of population aging. At present, the phenomenon of aging population has become a widespread concern of the whole society. Scientific and accurate prediction of aging population will help relevant departments to formulate specific countermeasures. This paper uses the Yearbook of China’s 1% population sampling survey in 2015 and the data published by the National Bureau of statistics. Based on the basic population prediction formula, the population prediction formula is established by using the index extrapolation method to predict the population aging development trend of provinces and cities in China from 2020 to 2050. The results show that: China’s aging degree will continue to increase, the size of the elderly population will continue to increase, 2020–2030 will be a period of rapid growth of the national population aging, after then the aging ratio will decline. The government should formulate security countermeasures for the elderly from various aspects as soon as possible and actively respond to aging the population.

Prevalence of Contraceptive Methods among Eligible Couples in an Urban Area of Chennai - A Cross Sectional Study

Introduction: Rapid population expansion is putting a strain on many developing countries' resources, especially in India. Optimal fertility management enables women and men to avoid and achieve conception and parenthood when desired. India launched officially Family Planning Programme way back in 1952 to address these issues, yet its goals were far from achieving facing stern obstacles in many forms. Surveys and studies by individual authors to find out the prevalence of contraceptive use and their determinants have been conducted in various parts of India. However, the contraceptive prevalence is not uniform across India. The aim of the study is to estimating the prevalence of contraception usage among eligible couples and to assess the factors associated with contraception usage. Methods: This was a cross sectional study conducted among married eligible couples living in the urban area named Semencheri in Chennai. It was carried out for a period of 4 months from 2ndApril to 5th of July 2019. The study population consisted of eligible married couples with female partner of age between 15 to 49yrs of age married for at least 2 year, and having minimum one child, Based on the results of a pilot study the sample size was calculated and estimated to be 120, structured questionnaire was used to collect data. Results: The prevalence of contraception was only 63.3% though 92.5% of couples studied were aware of the contraceptive methods, the factors like education of either of the couple and mode of delivery of the previous child were significantly associated with contraception usage. Conclusion: Even though the use of contraception has increased among couples, still there is an unmet need for contraception, in spite of increased education qualification and knowledge about contraceptive methods.

Library-based analysis reveals segment and length dependent characteristics of defective influenza genomes

Found in a diverse set of viral populations, defective interfering particles are parasitic variants that are unable to replicate on their own yet rise to relatively high frequencies. Their presence is associated with a loss of population fitness, both through the depletion of key cellular resources and the stimulation of innate immunity. For influenza A virus, these particles contain large internal deletions in the genomic segments which encode components of the heterotrimeric polymerase. Using a library-based approach, we comprehensively profile the growth and replication of defective influenza species, demonstrating that they possess an advantage during genome replication, and that exclusion during population expansion reshapes population composition in a manner consistent with their final, observed, distribution in natural populations. We find that an innate immune response is not linked to the size of a deletion; however, replication of defective segments can enhance their immunostimulatory properties. Overall, our results address several key questions in defective influenza A virus biology, and the methods we have developed to answer those questions may be broadly applied to other defective viruses.

A first investigation into the evolutionary relationships, population structure and demographic history of New Zealand Trevally (Pseudocaranx georgianus) and its implications for fisheries management

<p>Pseudocaranx georgianus is a commercially important fishery in New Zealand. Currently, the management of this fishery assumes that Quota Management Areas comprise single biological stocks of a single species. However, little is known regarding the population structure of New Zealand P. georgianus and morphological data suggests that a cryptic Pseudocaranx species is included within these fisheries. Whole genome sequence data was used to assemble and describe the first P. georgianus mitogenome. Primers were developed to produce the first genetic sequence data for New Zealand P. georgianus. The cytochrome c oxidase subunit I (COI) gene was sequenced for fourteen P. georgianus from New Zealand waters. These were compared phylogenetically with existing COI sequence data for P. georgianus from Australia and other Pseudocaranx species from a world-wide distribution. The hyper-variable control region of 304 P. georgianus sampled throughout New Zealand’s North Island and 68 P. georgianus from three locations in Western Australia were also sequenced. These sequences were used to explore the population structure and demographic history of New Zealand P. georgianus using haplotype networks, AMOVA’s, genetic diversity measures, Tajima’s D, Fu’s F and Bayesian migration analyses. The P. georgianus mitogenome is typical of Cartilaginous fish species showing no major gene rearrangements, typical gene region lengths and stop and start codons. While assembling the P. georgianus mitogenome, this thesis demonstrates the importance of key methodological choices made when assembling mitogenomes from whole genome sequence data in silco in Geneious version 11.1. The choice of reference mitogenome has the largest influence on the quality of the assembly, impacting the annotation of the final mitogenome and the resolution of uncertain DNA regions. Increasing the number of mapping iterations increased the quality of the assembly but has a limited ability to mitigate the effects of using a poor reference mitogenome. Overall, I demonstrate the need to investigate and report the quality of published mitogenomes. All Pseudocaranx species were monophyletic on the COI gene, supporting the current taxonomy of the Pseudocaranx complex. P. georgianus from Western Australia and New Zealand’s North Island represent a monophyletic clade pending a taxonomic verification that two Pseudocaranx dentex sampled in Australia are in fact P. georgianus. No evidence was found to suggest that either of the New Zealand or Western Australian populations of P. georgianus are isolated by distance or clearly structured as distinct stocks. However, some populations of New Zealand P. georgianus were genetically distinct, including fish sampled from Raglan and the Bay of Plenty (FST of 0.02698 (p-value: 0.00901+-0.0091) as well as the North Cape and North Taranaki Bight (FST: 0.02698, p-value: 0.00901+-0.0091). Some evidence was found to support the claim that P. georgianus along the west coast of New Zealand’s North Island is structured and no evidence was found to refute the claim that fish from the Bay of Plenty are the same biological stock as fish from TRE2. Highly divergent control region sequences of fish sampled from Three Kings Islands and the Kermadec Islands suggest that these fish could be a species distinct from P. georgianus. Two genetically distinct populations of P. georgianus were identified in New Zealand’s North Island and Western Australia (FST: 0.03517, p-value < 0.001), but further research would be required to determine if they are distinct species or populations. One juvenile population sampled in Whangarei had a high level of genetic connectivity with adult P. georgianus throughout New Zealand’s North Island, likely reflecting the batch spawning and occasional long-distance migration behaviour of P. georgianus. Negative Tajima’s D and Fu’s F statistics (D: -1.50612, p-value: 0.018; F: -23.54376, p-value: 0.011), unimodal mismatch distributions and skyline plots indicate that the New Zealand P. georgianus population has undergone a population expansion, possibly resulting from a geographic range expansion.The Western Australian population may also have undergone a population expansion (D: -1.27903, p-value: 0.086; F: -24.11497, p-value < 0.00001). However, a multimodal mismatch distribution (Harpending’s Raggedness index: 0.00454591, p-value: 0.02) indicated that there is some stability in the size of this population. This thesis is a first genetic investigation into New Zealand P. georgianus and has provided important biological insights into this species. Valuable information is revealed which will inform the management of New Zealand P. georgianus fisheries as inputs for stock assessment models. Additionally, several future research directions have been revealed which will further extend our knowledge of this taonga. For example, future genetic and taxonomic analyses may reveal a cryptic Pseudocaranx species occurring in the Three Kings and Kermadec Islands.</p>

A first investigation into the evolutionary relationships, population structure and demographic history of New Zealand Trevally (Pseudocaranx georgianus) and its implications for fisheries management

<p>Pseudocaranx georgianus is a commercially important fishery in New Zealand. Currently, the management of this fishery assumes that Quota Management Areas comprise single biological stocks of a single species. However, little is known regarding the population structure of New Zealand P. georgianus and morphological data suggests that a cryptic Pseudocaranx species is included within these fisheries. Whole genome sequence data was used to assemble and describe the first P. georgianus mitogenome. Primers were developed to produce the first genetic sequence data for New Zealand P. georgianus. The cytochrome c oxidase subunit I (COI) gene was sequenced for fourteen P. georgianus from New Zealand waters. These were compared phylogenetically with existing COI sequence data for P. georgianus from Australia and other Pseudocaranx species from a world-wide distribution. The hyper-variable control region of 304 P. georgianus sampled throughout New Zealand’s North Island and 68 P. georgianus from three locations in Western Australia were also sequenced. These sequences were used to explore the population structure and demographic history of New Zealand P. georgianus using haplotype networks, AMOVA’s, genetic diversity measures, Tajima’s D, Fu’s F and Bayesian migration analyses. The P. georgianus mitogenome is typical of Cartilaginous fish species showing no major gene rearrangements, typical gene region lengths and stop and start codons. While assembling the P. georgianus mitogenome, this thesis demonstrates the importance of key methodological choices made when assembling mitogenomes from whole genome sequence data in silco in Geneious version 11.1. The choice of reference mitogenome has the largest influence on the quality of the assembly, impacting the annotation of the final mitogenome and the resolution of uncertain DNA regions. Increasing the number of mapping iterations increased the quality of the assembly but has a limited ability to mitigate the effects of using a poor reference mitogenome. Overall, I demonstrate the need to investigate and report the quality of published mitogenomes. All Pseudocaranx species were monophyletic on the COI gene, supporting the current taxonomy of the Pseudocaranx complex. P. georgianus from Western Australia and New Zealand’s North Island represent a monophyletic clade pending a taxonomic verification that two Pseudocaranx dentex sampled in Australia are in fact P. georgianus. No evidence was found to suggest that either of the New Zealand or Western Australian populations of P. georgianus are isolated by distance or clearly structured as distinct stocks. However, some populations of New Zealand P. georgianus were genetically distinct, including fish sampled from Raglan and the Bay of Plenty (FST of 0.02698 (p-value: 0.00901+-0.0091) as well as the North Cape and North Taranaki Bight (FST: 0.02698, p-value: 0.00901+-0.0091). Some evidence was found to support the claim that P. georgianus along the west coast of New Zealand’s North Island is structured and no evidence was found to refute the claim that fish from the Bay of Plenty are the same biological stock as fish from TRE2. Highly divergent control region sequences of fish sampled from Three Kings Islands and the Kermadec Islands suggest that these fish could be a species distinct from P. georgianus. Two genetically distinct populations of P. georgianus were identified in New Zealand’s North Island and Western Australia (FST: 0.03517, p-value < 0.001), but further research would be required to determine if they are distinct species or populations. One juvenile population sampled in Whangarei had a high level of genetic connectivity with adult P. georgianus throughout New Zealand’s North Island, likely reflecting the batch spawning and occasional long-distance migration behaviour of P. georgianus. Negative Tajima’s D and Fu’s F statistics (D: -1.50612, p-value: 0.018; F: -23.54376, p-value: 0.011), unimodal mismatch distributions and skyline plots indicate that the New Zealand P. georgianus population has undergone a population expansion, possibly resulting from a geographic range expansion.The Western Australian population may also have undergone a population expansion (D: -1.27903, p-value: 0.086; F: -24.11497, p-value < 0.00001). However, a multimodal mismatch distribution (Harpending’s Raggedness index: 0.00454591, p-value: 0.02) indicated that there is some stability in the size of this population. This thesis is a first genetic investigation into New Zealand P. georgianus and has provided important biological insights into this species. Valuable information is revealed which will inform the management of New Zealand P. georgianus fisheries as inputs for stock assessment models. Additionally, several future research directions have been revealed which will further extend our knowledge of this taonga. For example, future genetic and taxonomic analyses may reveal a cryptic Pseudocaranx species occurring in the Three Kings and Kermadec Islands.</p>