cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5683/sp3/emzeje
title: Canadian Income Survey, 2018
title: CIS 2018
title: Enquête canadienne sur le revenu, 2018

description: &lt;p&gt;Income data has been used extensively by researchers to better understand the economic well-being of Canadians. To meet the needs of these users, Statistics Canada has produced numerous cross-sectional public use microdata files (PUMFs). PUMFs for the Survey of Consumer Finance (SCF) were released until reference year 1997. With the end of the SCF, PUMFs for the Survey of Labour and Income Dynamics (SLID) were produced for reference years 1996 to 2011.&lt;/p&gt; &lt;p&gt;The Canadian Income Survey (CIS) was introduced for the 2012 reference year. The CIS is a cross-sectional survey developed to provide information on the income and income sources of Canadians, with their individual and household characteristics. It is a short questionnaire which is asked of a sub-sample of respondents to the Labour Force Survey (LFS), gathering information on labour market activity, school attendance, support payments, child care expenses, inter-household transfers, personal income, and characteristics and costs of housing. The CIS content is supplemented with information from the LFS on individual and household characteristics (e.g. age, educational attainment, main job characteristics, and family type) and with tax data for income and income sources (Statistics Canada, 2018).&lt;/p&gt; &lt;p&gt;The CIS PUMF is an anonymized microdata file that contains only a subset of variables that are available on the CIS master file. Various techniques have been employed to protect CIS respondents against the risk of disclosure.&lt;/p&gt;
description: Canadian Income Survey
description: Migration from Nesstar
DOI: 10.5281/zenodo.18107629
title: Replication Package for the paper "Who Said CVE? How Vulnerability Identifiers Are Mentioned by Humans, Bots, and Agents in Pull Requests"

description: Replication Package for "Who Said CVE? How Vulnerabilities Are Mentioned in Human and Agent Authored Pull Requests"

This package contains the data files used to conduct our study.

Package Structure
The replication workflow consists of two main stages: extraction from the AIDev dataset and augmentation via the GitHub API.

To better understand our study, we briefly describe the structure of our package:

1. The script `scan_aidev_mentions.py` downloads the AIDev dataset and scans pull requests, commits and reviews for vulnerability patterns (e.g., CVE, CWE, GHSA). The output `aidev_vuln_mentions.csv` contains the raw mentions found in the dataset.

2. The script `augment_mentions.py` queries the GitHub API to find additional mentions in the same repositories as in the AIDev-pop dataset, but searches for different pull requests. The output `augmented_mentions.csv` contains data with actor types (human, bot and agent). 

3. The Jupyter Notebook `data_analysis.ipynb` loads the csv output files from the previous steps to compute statistics and generate the figures used in the paper.
DOI: 10.5281/zenodo.18351036
title: Replication Package for the paper "Who Said CVE? How Vulnerability Identifiers Are Mentioned by Humans, Bots, and Agents in Pull Requests"

description: Replication Package for "Who Said CVE? How Vulnerabilities Are Mentioned in Human and Agent Authored Pull Requests"

This package contains the data files used to conduct our study.

Package Structure
The replication workflow consists of two main stages: extraction from the AIDev dataset and augmentation via the GitHub API.

To better understand our study, we briefly describe the structure of our package:

1. The script `scan_aidev_mentions.py` downloads the AIDev dataset and scans pull requests, commits and reviews for vulnerability patterns (e.g., CVE, CWE, GHSA). The output `aidev_vuln_mentions.csv` contains the raw mentions found in the dataset.

2. The script `augment_mentions.py` queries the GitHub API to find additional mentions in the same repositories as in the AIDev-pop dataset, but searches for different pull requests. The output `augmented_mentions.csv` contains data with actor types (human, bot and agent). 

3. The Jupyter Notebook `data_analysis.ipynb` loads the csv output files from the previous steps to compute statistics and generate the figures used in the paper.
DOI: 10.6084/m9.figshare.28408393
title: Integrated taxonomy using morphology and DNA sequences: recognition of a new species with comments on the geological history of the <i>Liolaemus capillitas</i> clade (Squamata: Iguania)

description: The evolution of the Andean orogeny has an impact on the biota diversification of the region due to topographic changes and atmospheric circulation trajectories. Among them are the lizards of the Liolaemidae family and within this, of which <i>Liolaemus</i> is the genus with the most described species up to date, with approximately 290. One of the groups within the genus is the <i>Liolaemus elongatus</i> group, distributed in central-south of Argentina and Chile formed by four clades and a subclade: the <i>L. capillitas</i> subclade. In this work, we describe a new species belonging to the <i>L. capillitas</i> subclade, using an integrative approach, analysing both morphological (lepidosis, morphometrics, colouration and hemipenes characters) and molecular evidence (genetic distances and phylogeny). We made a divergence analysis of the representatives of the <i>L. elongatus</i> group. Furthermore, we correlated the ages of the geological events with the distribution areas for the lineages <i>L. capillitas</i> subclade. This newly described species shows character states (morphological and molecular) that allow its clear distinction from the other members of the <i>L. elongatus</i> group, as well as from the rest of <i>Liolaemus</i>. The divergence analysis places the new species in the <i>L. capillitas</i> subclade and allows us to infer the successive geological events that served as physical barriers to the diversification of the group, besides explaining the current distribution of the group. http://zoobank.org/urn:lsid:zoobank.org:pub:EDFA2340-46D2-460A-AA31-C914E5288883
DOI: 10.6084/m9.figshare.28408393.v1
title: Integrated taxonomy using morphology and DNA sequences: recognition of a new species with comments on the geological history of the <i>Liolaemus capillitas</i> clade (Squamata: Iguania)

description: The evolution of the Andean orogeny has an impact on the biota diversification of the region due to topographic changes and atmospheric circulation trajectories. Among them are the lizards of the Liolaemidae family and within this, of which <i>Liolaemus</i> is the genus with the most described species up to date, with approximately 290. One of the groups within the genus is the <i>Liolaemus elongatus</i> group, distributed in central-south of Argentina and Chile formed by four clades and a subclade: the <i>L. capillitas</i> subclade. In this work, we describe a new species belonging to the <i>L. capillitas</i> subclade, using an integrative approach, analysing both morphological (lepidosis, morphometrics, colouration and hemipenes characters) and molecular evidence (genetic distances and phylogeny). We made a divergence analysis of the representatives of the <i>L. elongatus</i> group. Furthermore, we correlated the ages of the geological events with the distribution areas for the lineages <i>L. capillitas</i> subclade. This newly described species shows character states (morphological and molecular) that allow its clear distinction from the other members of the <i>L. elongatus</i> group, as well as from the rest of <i>Liolaemus</i>. The divergence analysis places the new species in the <i>L. capillitas</i> subclade and allows us to infer the successive geological events that served as physical barriers to the diversification of the group, besides explaining the current distribution of the group. http://zoobank.org/urn:lsid:zoobank.org:pub:EDFA2340-46D2-460A-AA31-C914E5288883
DOI: 10.6084/m9.figshare.28451622
title: Evolution and biogeography of <i>Litorogammarus</i> Marin, Palatov & Copilaș-Ciocianu, 2023 (Amphipoda: Gammaridae) with description of two new Caspian endemic species

description: The extensive radiation of gammaroidean amphipods in the brackish Ponto-Caspian region gave rise to almost 100 species occupying a wide range of ecological niches and exhibiting striking morphological diversity. However, much of this fauna remains poorly known. Here, we examine the origin and evolutionary timescale of the genus <i>Litorogammarus</i> and describe two new endemic species from the Caspian Sea by integrating multilocus phylogenetics, fossil-based molecular clock calibration, and morphological observations. We show that the genus originated in the Paratethys during the Late Miocene and that its major lineages arose during the Pliocene when the Paratethys split into the Black and Caspian seas. Both newly described Caspian species (<i>L. glareophilus</i> sp. nov. and <i>L. samuricus</i> sp. nov.) split from their Black Sea endemic sister species during the last two million years, coinciding with two chronologically distinct periods of isolation following major transgressive episodes (Apsheronian and Bakunian/Chaudian). Our results further confirm the evolutionary importance of the recurrent isolation-reconnection episodes between the Black and Caspian seas throughout the Pleistocene, which we herein interpret as functioning like a “species pump”. http://zoobank.org/urn:lsid:zoobank.org:pub:41A6311F-09A8-47A3-91D0-01D409F8F7AB
DOI: 10.6084/m9.figshare.28451622.v1
title: Evolution and biogeography of <i>Litorogammarus</i> Marin, Palatov & Copilaș-Ciocianu, 2023 (Amphipoda: Gammaridae) with description of two new Caspian endemic species

description: The extensive radiation of gammaroidean amphipods in the brackish Ponto-Caspian region gave rise to almost 100 species occupying a wide range of ecological niches and exhibiting striking morphological diversity. However, much of this fauna remains poorly known. Here, we examine the origin and evolutionary timescale of the genus <i>Litorogammarus</i> and describe two new endemic species from the Caspian Sea by integrating multilocus phylogenetics, fossil-based molecular clock calibration, and morphological observations. We show that the genus originated in the Paratethys during the Late Miocene and that its major lineages arose during the Pliocene when the Paratethys split into the Black and Caspian seas. Both newly described Caspian species (<i>L. glareophilus</i> sp. nov. and <i>L. samuricus</i> sp. nov.) split from their Black Sea endemic sister species during the last two million years, coinciding with two chronologically distinct periods of isolation following major transgressive episodes (Apsheronian and Bakunian/Chaudian). Our results further confirm the evolutionary importance of the recurrent isolation-reconnection episodes between the Black and Caspian seas throughout the Pleistocene, which we herein interpret as functioning like a “species pump”. http://zoobank.org/urn:lsid:zoobank.org:pub:41A6311F-09A8-47A3-91D0-01D409F8F7AB
DOI: 10.6084/m9.figshare.28607440
title: A deceptive variety: integrative systematics and phylogeography suggest <i>Adalaria proxima</i> and <i>Adalaria loveni</i> represent a single species (Gastropoda: Nudibranchia)

description: In this paper we provide a thorough morphological re-examination of the type species of the genus <i>Adalaria</i> (Gastropoda: Onchidorididae), <i>Adalaria loveni</i>, and its closely related species <i>Adalaria proxima</i> in boreal and subarctic seas, together with a molecular phylogeny, and an analysis of the population structure of these lineages. The external morphology, spicule composition, and features of the buccal armature and the reproductive system were studied using light microscopy, scanning electron microscopy and micro-CT scan technology. The molecular study included the inference of phylogenetic relationships within the family Onchidorididae based on two mitochondrial and three nuclear markers, as well as a COI-based haplotype network reconstruction. Our results show that <i>Adalaria proxima</i> is a trans-Arctic species and conspecific with <i>A. loveni</i>, with a wide geographic range and a high degree of morphological variability, both in colour and morphology of the notal tubercules. Our analysis does not support the monophyly of the genus <i>Adalaria</i>, but we consider it to be premature to introduce new generic names or redefine the concept of <i>Adalaria</i> until a comprehensive phylogeny at species level is available. Two distinct haplogroups were identified in <i>A. proxima</i>; one with individuals from the Pacific, Canadian Arctic, and northwestern Atlantic, and the other with individuals from the northeastern Atlantic and adjacent subarctic regions. This suggests restricted gene flow between the North-East and the North-West Atlantic, with potential genetic exchange between the North-West Atlantic and Pacific populations. One notable characteristic of <i>Adalaria proxima</i> populations is their significant variability in both external and internal morphology.
DOI: 10.6084/m9.figshare.28607440.v1
title: A deceptive variety: integrative systematics and phylogeography suggest <i>Adalaria proxima</i> and <i>Adalaria loveni</i> represent a single species (Gastropoda: Nudibranchia)

description: In this paper we provide a thorough morphological re-examination of the type species of the genus <i>Adalaria</i> (Gastropoda: Onchidorididae), <i>Adalaria loveni</i>, and its closely related species <i>Adalaria proxima</i> in boreal and subarctic seas, together with a molecular phylogeny, and an analysis of the population structure of these lineages. The external morphology, spicule composition, and features of the buccal armature and the reproductive system were studied using light microscopy, scanning electron microscopy and micro-CT scan technology. The molecular study included the inference of phylogenetic relationships within the family Onchidorididae based on two mitochondrial and three nuclear markers, as well as a COI-based haplotype network reconstruction. Our results show that <i>Adalaria proxima</i> is a trans-Arctic species and conspecific with <i>A. loveni</i>, with a wide geographic range and a high degree of morphological variability, both in colour and morphology of the notal tubercules. Our analysis does not support the monophyly of the genus <i>Adalaria</i>, but we consider it to be premature to introduce new generic names or redefine the concept of <i>Adalaria</i> until a comprehensive phylogeny at species level is available. Two distinct haplogroups were identified in <i>A. proxima</i>; one with individuals from the Pacific, Canadian Arctic, and northwestern Atlantic, and the other with individuals from the northeastern Atlantic and adjacent subarctic regions. This suggests restricted gene flow between the North-East and the North-West Atlantic, with potential genetic exchange between the North-West Atlantic and Pacific populations. One notable characteristic of <i>Adalaria proxima</i> populations is their significant variability in both external and internal morphology.
DOI: 10.6084/m9.figshare.29039428
title: Systematics of Amydetinae (Coleoptera: Lampyridae)

description: Amydetinae is a subfamily of Neotropical fireflies with 53 species distributed in three genera. Amydetine diversity is underestimated and understudied, and its taxonomy is yet to be clarified by phylogenetic studies. <i>Amydetes</i> and <i>Memoan</i> are exclusively South American, but <i>Magnoculus</i> spans South and Central America. The enigmatic <i>Cheguevaria</i>, the type of Cheguevariinae, has been recovered close to <i>Magnoculus</i>, but their relationship to <i>Amydetes</i> and <i>Memoan</i> remains elusive since these were never included together in phylogenetic analyses. Here, we inferred the first phylogenetic relationships of Amydetinae using 38 taxa – covering 10 of 12 subfamilies – and 87 morphological characters. Our matrix included all three Amydetinae genera, as well as historically related genera, in addition to three new genera and five new species. <i>Cheguevaria</i> is consistently recovered in – not sister to – Amydetinae, suggesting this is a highly modified Caribbean member of this lineage and putting into question the Cheguevariinae subfamily status. <i>Photoctus</i> is also consistently recovered in Amydetinae, confirming its placement in this subfamily for the first time under a phylogenetic framework. Our results support a redefinition of Amydetinae sensu novum. Thus, we propose new definitions and diagnoses for Amydetinae and its constituent genera. We also redescribe the type species of the genera <i>Magnoculus</i> and <i>Photoctus</i>, to inform updated diagnoses and help stabilize the taxonomy of Amydetine genera. We also present an identification key for Amydetinae s.n. genera. http://zoobank.org/urn:lsid:zoobank.org:pub:CBB20012-AB5F-49FD-93B1-37F1AE9A730A
DOI: 10.6084/m9.figshare.29039428.v1
title: Systematics of Amydetinae (Coleoptera: Lampyridae)

description: Amydetinae is a subfamily of Neotropical fireflies with 53 species distributed in three genera. Amydetine diversity is underestimated and understudied, and its taxonomy is yet to be clarified by phylogenetic studies. <i>Amydetes</i> and <i>Memoan</i> are exclusively South American, but <i>Magnoculus</i> spans South and Central America. The enigmatic <i>Cheguevaria</i>, the type of Cheguevariinae, has been recovered close to <i>Magnoculus</i>, but their relationship to <i>Amydetes</i> and <i>Memoan</i> remains elusive since these were never included together in phylogenetic analyses. Here, we inferred the first phylogenetic relationships of Amydetinae using 38 taxa – covering 10 of 12 subfamilies – and 87 morphological characters. Our matrix included all three Amydetinae genera, as well as historically related genera, in addition to three new genera and five new species. <i>Cheguevaria</i> is consistently recovered in – not sister to – Amydetinae, suggesting this is a highly modified Caribbean member of this lineage and putting into question the Cheguevariinae subfamily status. <i>Photoctus</i> is also consistently recovered in Amydetinae, confirming its placement in this subfamily for the first time under a phylogenetic framework. Our results support a redefinition of Amydetinae sensu novum. Thus, we propose new definitions and diagnoses for Amydetinae and its constituent genera. We also redescribe the type species of the genera <i>Magnoculus</i> and <i>Photoctus</i>, to inform updated diagnoses and help stabilize the taxonomy of Amydetine genera. We also present an identification key for Amydetinae s.n. genera. http://zoobank.org/urn:lsid:zoobank.org:pub:CBB20012-AB5F-49FD-93B1-37F1AE9A730A
DOI: 10.6084/m9.figshare.29040427.v1
title: Integrative systematics of the Brazilian tree “sucupira”: morphological, cytogenetic and genomic boundaries of <i>Pterodon emarginatus</i> Vogel and <i>P. pubescens</i> (Benth.) Benth. (Leguminosae, Papilionoideae)

description: In the genus <i>Pterodon</i> (Leguminosae, Papilionoideae) <i>P. emarginatus</i> and <i>P. pubescens</i> (both known as “sucupira”) exhibit unclear boundaries due to their incomplete isolation barriers and phylogenetic proximity. Both species have a conserved karyotype with 2<i>n</i> = 16, featuring small and morphologically similar chromosomes, and they form hybrids in sympatric areas of distribution in the Neotropical Savanna. Here, we aimed to revisit the systematics of <i>P. emarginatus</i> and <i>P. pubescens</i> based on morphometry of vegetative and reproductive characters, cytogenetics and genome skimming (low coverage Illumina sequencing). The morphometric analysis based on continuous data resulted in unclear distinctiveness between <i>P. emarginatus</i> and <i>P. pubescens</i>. However, the discrete characters of pubescence on leaves and flowers allow us to distinguish these species and individuals with intermediate morphology. The species presented similar genome sizes (1 C = ca. 0.64 pg) and stable karyotypes with two pairs of CMA<sup>+</sup>/DAPI<sup>−</sup> bands/35S rDNA and one pair of 5S rDNA sites. Similarities were also observed in the repetitive genomic fraction (∼25%) with few differences in the retrotransposons (RTs) abundances. The most representative RTs in both species were Ty1/copia-SIRE, Ty3/gypsy-Athila and Ty3/gypsy-Tekay. Remarkably, we found a difference in the 5S rDNA cluster, with the nontranscribed spacer (NTS) regions varying in length and similarity between <i>P. emarginatus</i> and <i>P. pubescens</i>. Six satellite DNAs were found, two of which were exclusive to <i>P. emarginatus</i> and four were shared by both species. <i>In situ</i> hybridization revealed that the most abundant repeats were enriched in proximal CMA<sup>+</sup> heterochromatin in both species, except for the Ty1/copia-Ale retroelement, which was widely dispersed across all <i>P. pubescens</i> chromosomes. Our morphological, cytogenetic and genomic data revealed that <i>Pterodon</i> species boundaries are complex corroborating the evolutionary proximity between these species. We suggest that the cytogenetic and genomic stability found in <i>Pterodon</i> may facilitate the natural interspecific gene flow reported in sympatric populations, complicating the interpretation of morphological traits and the understanding of their systematics and evolution.
DOI: 10.6084/m9.figshare.30888523
title: Revisiting Chilean gorgonians (Cnidaria: Octocorallia: Gorgoniidae): taxonomic clarification and molecular phylogeny of <i>Leptogorgia chilensis</i> and <i>Phycogorgia fucata</i>

description: Most biodiversity studies of eastern Pacific octocorals have focused on the tropical shallow waters from Mexico to Peru, and more recently, on those off Chile. The first description of a Chilean octocoral dates back to the H.M.S. Challenger expedition (1873–1876), and since then, only a few descriptions of new coral species have been published from this region. In addition, the taxonomic status of most gorgonians reported from the temperate Pacific coast of South America remains uncertain due to the loss of the original type material. In this study, we use morphological characters and nuclear and mitochondrial markers to re-evaluate the taxonomy of the Chilean gorgonians <i>Phycogorgia fucata</i> and <i>Leptogorgia chilensis</i>. Our findings support the monophyly of Chilean <i>Leptogorgia</i>, confirm that <i>Leptogorgia chilensis</i> from Chile is distinct from specimens identified as the same species in California, and reveal that <i>P. fucata</i>, despite its unique morphology, should be included in the genus <i>Leptogorgia</i>.
DOI: 10.6084/m9.figshare.30888523.v2
title: Revisiting Chilean gorgonians (Cnidaria: Octocorallia: Gorgoniidae): taxonomic clarification and molecular phylogeny of <i>Leptogorgia chilensis</i> and <i>Phycogorgia fucata</i>

description: Most biodiversity studies of eastern Pacific octocorals have focused on the tropical shallow waters from Mexico to Peru, and more recently, on those off Chile. The first description of a Chilean octocoral dates back to the H.M.S. Challenger expedition (1873–1876), and since then, only a few descriptions of new coral species have been published from this region. In addition, the taxonomic status of most gorgonians reported from the temperate Pacific coast of South America remains uncertain due to the loss of the original type material. In this study, we use morphological characters and nuclear and mitochondrial markers to re-evaluate the taxonomy of the Chilean gorgonians <i>Phycogorgia fucata</i> and <i>Leptogorgia chilensis</i>. Our findings support the monophyly of Chilean <i>Leptogorgia</i>, confirm that <i>Leptogorgia chilensis</i> from Chile is distinct from specimens identified as the same species in California, and reveal that <i>P. fucata</i>, despite its unique morphology, should be included in the genus <i>Leptogorgia</i>.