A glimpse into mollusk genomics from the de novo genome of Arion vulgaris MoquinTandon, 1855 (Gastropoda, Stylommatophora)

Mollusks are among nature’s greatest innovators, representing some of the most ancient and evolutionary successful animals, with a tremendous diversity in morphology, behavior, lifestyle and habitats. Since the beginning of human civilization, this taxon has received a great deal of attention, for example as ornaments, currency, and diet, and is nowadays closely linked to the economy, health and ecology of human society. For more than two centuries, malacologists have laid a solid foundation for our understanding on the evolution of the phylum Mollusca through behavioral and environmental observations, as well as morphological and anatomical studies. The beginning of the era of genetic and genomic reconstruction of natural history has allowed gaining a complementary perspective on molluscan diversity and evolution. A genome contains the complete genetic information of an organism or a cell, passed from one generation to the next. A reference genome, i.e., a representative nucleic acid sequence database of a target species, reveals the structure, organization and functional features of genes, and therefore serves as a foundation for molecular and genomic studies. Recent improvements in sequencing technologies have provided the ability to produce high-quality genome assemblies in a shorter period of time and with affordable costs. However, relative to the huge number of extant species, molluscan genomic resources lag far behind, and are highly uneven across classes and taxa. For example, up to now (August 2022) no sequenced and assembled genomes are available for four out of the eight mollusk classes (Scaphopoda, Solenogastres, Caudofoveata, Monoplacophora). Gastropods account for 80% of extant species in the phylum Mollusca. While the total number of reported gastropod genomes (49) accounts for 45% of published mollusk genomes, this only represents 0.05% of all known gastropod species. During the course of my dissertation, we generated whole-genome and transcriptome data for Arion vulgaris Moquin-Tandon, 1855 (Mollusca: Gastropoda: Stylommatophora), a notorious agricultural pest in Europe and thus an ecologically and economically important species. We assembled a chromosome-level genome of A. vulgaris with considerable completeness and contiguous, annotated genes and repetitive elements, as well as its mitochondrial genome. Using the mitogenome, we explored the mitochondrial evolutionary patterns as well as phylogenetic relationships of stylommatophoran land snails and slugs. Using whole-genome data, we identified single-copy orthologous genes among major gastropod groups, and recovered Psilogastropoda s.l., that is Patellogastropoda as sister to Vetigastropoda and Neomphalina, for deep gastropod phylogeny. As the first reported genome of a land slug, we have also made extensive comparisons between the genome of Arion vulgaris with land snails and other aquatic and marine species of the clade Heterobranchia. We identified genes that are specific/expanded/positively selected in A. vulgaris, which show functional relatedness to its strong adaptive capacities. Furthermore, we showed that the whole-genome duplication event that occurred approximately 93–109 Mya shared by Stylommatophora species might have promoted stylommatophoran land invasion, speciation, and adaptive radiation. Small-scale gene duplication, i.e., a formidable recent expansion of transposable elements of A. vulgaris, might have additionally driven its genetic innovation and quick adaptation, promoting invasion of new areas and success in changing habitats and environments

Labor Market Conditions and Fertility in Japan

This thesis aims to study the relation between fertility behavior and labor market in Japan. The slack youth employment market has been blamed for the continuously declining fertility rate. However, the linkage between labor market fluctuation and fertility behavior is empirically unclear. Based on the micro data compiled from Japanese Generally Social Survey, I apply discrete time hazard model and possion regression. The empirical result shows that contemporaneous labor market fluctuation negatively impacts on the relative risk of first childbirth while has no significant influence on continuous births. However, the employment opportunities at labor market entry, which have continuous influence on sequent income, have little impact on women’s total number of children. I also find that male and female unemployment affect female fertility in the same direction, though the strengths vary. Additionally, reactions of fertility behaviors are different across education backgrounds. E.g., when the unemployment rate increases, the relative risk of first childbirths for well-educated women diminishes more than that of low educated ones

Getting old in a changing world : Sons, pension, and the wellbeing of the elderly in contemporary China

The Chinese population is rapidly aging, which has brought challenges for the elderly support system. Until very recently, only urban employees were eligible to receive a pension, while the rural elderly were forced to rely on income from their own labor and support from their family. In these circumstances, it is unsurprising that the rural elderly were most likely to fall into poverty. The recent introduction of the New Rural Social Pension represents a fundamental change, as it offer a comprehensive pension to rural Chinese for the first time in its history. The initiative may reduce the need for family support. Son preference is well-established in China as, traditionally, sons are expected to be mainly responsible for taking care of their elderly parents. As the new pension relieves the elderly’s economic dependency on their children, it becomes relevant to ask whether it has mediated the implications of son preference, notably whether having a son still results in a better later life. This dissertation explores how changes in intergenerational support have affected the elderly’s wellbeing. The results show that the new pension has made it possible for the rural elderly to retire and improved their relative bargaining power within the household – allowing them to spend more on healthcare. The treatment effect of the pension is remarkably strong given the small amount of benefit (9 USD per month). This indicates that the rural elderly had been living in very poor conditions, and suggests that the family support system cannot adequately provide for them. It appears that better public support is required.Another finding concerns the situation within the family. My results show that having a son does not improve either material support or subjective wellbeing. It therefore appears that young parents’ son preference does not turn out to be a rational choice in later life. Moreover, the expansion of social welfare has weakened the economic rational of favoring sons, and increased the importance of daughters, as parents’ needs shift from day-to-day care to emotional support. Once basic material needs are met, daughters’ have the advantage of providing emotional support, and they become essential to their parents

Labor Supply Responses to New Rural Pension Insurances in China: A Regression Discontinuity Approach

Transitioning into retirement is an under-researched phenomenon in developing countries. Largely, this is linked to a predominance of contexts where –in particular –the rural population remains outside the coverage of any formal pension system. In 2008, China introduced the New Rural Social Pension (NRSP), a program which by now covers the majority of the Chinese rural elderly. This paper examines the effects of the NRSP on the labor supply of the elderly in rural China. As pension benefit eligibility at the time of its implementation is conditional on age, a regression discontinuity design is applied to investigate the casual effect of the receipt of pension benefits on labor supply. Furthermore, as the NRSP isneither means-tested nor conditions on retirement, it induces a pure income effect on employment. Using data from the China Health and Retirement Longitudinal Study, a nationally representative data set, we find that the receipt of pension benefitsincreases the probability of retirement among the rural elderly by around 15%

Eccentricity to the rescue! Detecting Accelerating Eccentric Binaries in the LISA Band

Many gravitational wave (GW) sources in the LISA band are expected to have non-negligible eccentricity. Furthermore, many of them can undergo acceleration because they reside in the presence of a tertiary. Here we develop analytical and numerical methods to quantify how the compact binary's eccentricity enhances the detection of its peculiar acceleration. We show that the general relativistic precession pattern can disentangle the binary's acceleration-induced frequency shift from the chirp-mass-induced frequency shift in GW template fitting, thus relaxing the signal-to-noise ratio requirement for distinguishing the acceleration by a factor of $10\sim100$. Moreover, by adopting the GW templates of the accelerating eccentric compact binaries, we can enhance the acceleration measurement accuracy by a factor of $\sim100$, compared to the zero-eccentricity case, and detect the source's acceleration even if it does not change during the observational time. For example, a stellar-mass binary black hole (BBH) with moderate eccentricity in the LISA band yields an error of the acceleration measurement $\sim10^{-7}m\cdot s^{-2}$ for $\rm{SNR}=20$ and observational time of $4$ yrs. In this example, we can measure the BBHs' peculiar acceleration even when it is $\sim1\rm pc$ away from a $4\times 10^{6}\rm M_{\odot}$ SMBH. Our results highlight the importance of eccentricity to the LISA-band sources and show the necessity of developing GW templates for accelerating eccentric compact binaries.Comment: 14 pages (+references), 9 figures. Submitted to PR

Beyond Semantics: Learning a Behavior Augmented Relevance Model with Self-supervised Learning

Relevance modeling aims to locate desirable items for corresponding queries, which is crucial for search engines to ensure user experience. Although most conventional approaches address this problem by assessing the semantic similarity between the query and item, pure semantic matching is not everything.Comment: Partial conten

In ChatGPT We Trust? Measuring and Characterizing the Reliability of ChatGPT

The way users acquire information is undergoing a paradigm shift with the advent of ChatGPT. Unlike conventional search engines, ChatGPT retrieves knowledge from the model itself and generates answers for users. ChatGPT's impressive question-answering (QA) capability has attracted more than 100 million users within a short period of time but has also raised concerns regarding its reliability. In this paper, we perform the first large-scale measurement of ChatGPT's reliability in the generic QA scenario with a carefully curated set of 5,695 questions across ten datasets and eight domains. We find that ChatGPT's reliability varies across different domains, especially underperforming in law and science questions. We also demonstrate that system roles, originally designed by OpenAI to allow users to steer ChatGPT's behavior, can impact ChatGPT's reliability. We further show that ChatGPT is vulnerable to adversarial examples, and even a single character change can negatively affect its reliability in certain cases. We believe that our study provides valuable insights into ChatGPT's reliability and underscores the need for strengthening the reliability and security of large language models (LLMs)