[ { "id": "https://authors.library.caltech.edu/records/memc7-9g637", "eprint_id": 113577, "eprint_status": "archive", "datestamp": "2023-08-20 04:09:35", "lastmod": "2023-12-22 23:33:32", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Beery-Sara", "name": { "family": "Beery", "given": "Sara" }, "orcid": "0000-0002-2544-1844" }, { "id": "Cole-Elijah", "name": { "family": "Cole", "given": "Elijah" } }, { "id": "Parker-J", "name": { "family": "Parker", "given": "Joseph" }, "orcid": "0000-0001-9598-2454" }, { "id": "Perona-P", "name": { "family": "Perona", "given": "Pietro" }, "orcid": "0000-0002-7583-5809" }, { "id": "Winner-Kevin", "name": { "family": "Winner", "given": "Kevin" } } ] }, "title": "Species Distribution Modeling for Machine Learning Practitioners: A Review", "ispublished": "unpub", "full_text_status": "public", "keywords": "species distribution modeling, ecological niche modeling, machine learning", "note": "Our research for this paper included informational interviews with Meredith Palmer, Michael Tabak, Corrie Moreau, and Carrie Seltzer. Their insights into the unique challenges of species distribution modeling was invaluable. This work was supported in part by the Caltech Resnick Sustainability Institute and NSFGRFP Grant No. 1745301. The views expressed in this work are those of the authors and do not necessarily reflect the views of the NSF.\n\n
Submitted - 2107.10400.pdf
", "abstract": "Conservation science depends on an accurate understanding of what's happening in a given ecosystem. How many species live there? What is the makeup of the population? How is that changing over time? Species Distribution Modeling (SDM) seeks to predict the spatial (and sometimes temporal) patterns of species occurrence, i.e. where a species is likely to be found. The last few years have seen a surge of interest in applying powerful machine learning tools to challenging problems in ecology. Despite its considerable importance, SDM has received relatively little attention from the computer science community. Our goal in this work is to provide computer scientists with the necessary background to read the SDM literature and develop ecologically useful ML-based SDM algorithms. In particular, we introduce key SDM concepts and terminology, review standard models, discuss data availability, and highlight technical challenges and pitfalls.", "date": "2022-03-01", "date_type": "published", "publisher": "arXiv", "id_number": "CaltechAUTHORS:20220224-200801611", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20220224-200801611", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Resnick Sustainability Institute" }, { "agency": "NSF Graduate Research Fellowship", "grant_number": "DGE-1745301" } ] }, "local_group": { "items": [ { "id": "Resnick-Sustainability-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.48550/arXiv.2107.10400", "primary_object": { "basename": "2107.10400.pdf", "url": "https://authors.library.caltech.edu/records/memc7-9g637/files/2107.10400.pdf" }, "resource_type": "monograph", "pub_year": "2022", "author_list": "Beery, Sara; Cole, Elijah; et el." }, { "id": "https://authors.library.caltech.edu/records/352fh-hax53", "eprint_id": 111335, "eprint_status": "archive", "datestamp": "2023-08-20 05:29:23", "lastmod": "2023-12-22 23:38:57", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Perry-Elena-K", "name": { "family": "Perry", "given": "Elena K." }, "orcid": "0000-0002-7151-1479" }, { "id": "Siozios-Stefanos", "name": { "family": "Siozios", "given": "Stefanos" }, "orcid": "0000-0002-1104-7061" }, { "id": "Hurst-Gregory-D-D", "name": { "family": "Hurst", "given": "Gregory D. D." }, "orcid": "0000-0002-7163-7784" }, { "id": "Parker-J", "name": { "family": "Parker", "given": "Joseph" }, "orcid": "0000-0001-9598-2454" } ] }, "title": "Structure of an ant-myrmecophile-microbe community", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. \n\nWe thank Clive Turner (UK) for providing living specimens of Pella cognata and Lasius fuliginosus, Tim Struyve (Belgium) for providing Drusilla canaliculata and Julian Wagner (Caltech) for Lissagria laeviuscula. Preliminary stages of this work were facilitated by a seed grant from Caltech's Center for Environmental Microbial Interactions, and we greatly appreciate the support and generosity of Dianne Newman (Caltech) throughout the course of this study. This work was funded by an Army Research Office MURI award, W911NF1910269, to J. Parker.\n\nThe authors have declared no competing interest.\n\nSubmitted - 2021.10.04.462948v1.full.pdf
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", "abstract": "Superorganismal ant colonies play host to a menagerie of symbiotic arthropods, termed myrmecophiles, which exhibit varying degrees of social integration into colony life. Such systems permit examination of how animal community interactions influence microbial assemblages. Here, we present an ecologically and phylogenetically comprehensive characterization of an ant-myrmecophile-microbe community in Southern California. Using 16S rRNA profiling, we find that microbiotas of the velvety tree ant (Liometopum occidentale) and its cohort of myrmecophiles are distinguished by species-specific characteristics but nevertheless bear signatures of their behavioral interactions. We found that the host ant microbiome was diverse at all taxonomic levels; that of a myrmecophilous cricket was moderately diverse, while microbiotas of three myrmecophilous rove beetles (Staphylinidae), which have convergently evolved symbiosis with Liometopum, were dominated by intracellular endosymbionts. Yet, despite these compositional differences, similarities between ant and myrmecophile microbiotas correlated with the nature and intimacy of their behavioral relationships. Physical interactions such as grooming and trophallaxis likely facilitate cross-species extracellular microbial sharing. Further, phylogenetic comparisons of microbiotas from myrmecophile rove beetles and outgroups revealed a lack of co-cladogenesis of beetles and intracellular endosymbionts, and limited evidence for convergence among the myrmecophiles' intracellular microbiotas. Comparative genomic analyses of the dominant Rickettsia endosymbiont of the most highly socially integrated myrmecophile imply possible functions unrelated to nutrient-provisioning in the host beetle's specialized lifestyle. Our findings indicate that myrmecophile microbiotas evolve largely independently of the constraints of deep evolutionary history, and that the transition to life inside colonies, including social interactions with hosts, plays a significant role in structuring bacterial assemblages of these symbiotic insects.", "date": "2021-10-05", "date_type": "published", "id_number": "CaltechAUTHORS:20211008-224629828", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211008-224629828", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Caltech Center for Environmental Microbial Interactions (CEMI)" }, { "agency": "Army Research Office (ARO)", "grant_number": "W911NF1910269" } ] }, "local_group": { "items": [ { "id": "Caltech-Center-for-Environmental-Microbial-Interactions-(CEMI)" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2021.10.04.462948", "primary_object": { "basename": "2021.10.04.462948v1.full.pdf", "url": "https://authors.library.caltech.edu/records/352fh-hax53/files/2021.10.04.462948v1.full.pdf" }, "related_objects": [ { "basename": "media-1.mov", "url": "https://authors.library.caltech.edu/records/352fh-hax53/files/media-1.mov" }, { "basename": "media-2.xlsx", "url": "https://authors.library.caltech.edu/records/352fh-hax53/files/media-2.xlsx" }, { "basename": "media-3.pdf", "url": "https://authors.library.caltech.edu/records/352fh-hax53/files/media-3.pdf" }, { "basename": "media-4.xlsx", "url": "https://authors.library.caltech.edu/records/352fh-hax53/files/media-4.xlsx" }, { "basename": "media-5.xls", "url": "https://authors.library.caltech.edu/records/352fh-hax53/files/media-5.xls" }, { "basename": "media-6.zip", "url": "https://authors.library.caltech.edu/records/352fh-hax53/files/media-6.zip" } ], "resource_type": "monograph", "pub_year": "2021", "author_list": "Perry, Elena K.; Siozios, Stefanos; et el." }, { "id": "https://authors.library.caltech.edu/records/24wrg-rx971", "eprint_id": 112505, "eprint_status": "archive", "datestamp": "2023-08-20 03:16:34", "lastmod": "2023-12-13 17:10:18", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Br\u00fcckner-A-K", "name": { "family": "Br\u00fcckner", "given": "Adrian" }, "orcid": "0000-0002-9184-8562" }, { "id": "Badroos-Jean-M", "name": { "family": "Badroos", "given": "Jean M." }, "orcid": "0000-0002-0867-3686" }, { "id": "Learsch-Robert-W", "name": { "family": "Learsch", "given": "Robert W." }, "orcid": "0000-0001-6329-5879" }, { "id": "Yousefelahiyeh-Mina", "name": { "family": "Yousefelahiyeh", "given": "Mina" }, "orcid": "0000-0003-0365-3018" }, { "id": "Kitchen-Sheila-A", "name": { "family": "Kitchen", "given": "Sheila A." }, "orcid": "0000-0003-4402-8139" }, { "id": "Parker-J", "name": { "family": "Parker", "given": "Joseph" }, "orcid": "0000-0001-9598-2454" } ] }, "title": "Evolutionary assembly of cooperating cell types in an animal chemical defense system", "ispublished": "unpub", "full_text_status": "public", "note": "Posted May 15, 2021.\n\nAuthor contributions: AB and JP designed the study. AB performed experiments with help from JP (microdissections), JMB (in vitro protein studies) and MY (microinjections). RWL performed rheological measurements and processed raw data, AB analyzed the data with input from SAK. SAK performed GO-term analysis. JP supervised the project. AB and JP wrote the manuscript with input from SAK, JMB and RWL. All authors discussed and commented on the manuscript.\n\nAcknowledgements: We thank Yuriko Kishi, Tom Naragon and Julian Wagner for help with in situ HCR, transcriptome assembly and bioinformatics, respectively; Fan Gao, Lior Pachter and the Bioinformatics Resource Center at Caltech; Sisi Chen, Jong H. Park, Matt Thomson and the Single Cell Profiling and Engineering Center (SPEC) in the Beckman Institute at Caltech; Melanie Spero for help with bacterial experiments and Chelsey M. VanDrisse for providing reagents. We are grateful to Marianne Bronner, Michael Dickinson, Lior Pachter and members of the Parker lab for feedback on this paper. AB is a Simons Fellow of the Life Sciences Research Foundation (LSRF). This work was supported by a Rita Allen Foundation Scholars Award, an Alfred P. Sloan Research Fellowship, a Shurl and Kay Curci Foundation grant, a Klingenstein-Simons Fellowship Award and a National Science Foundation CAREER award (NSF 2047472) to JP.\n\nData availability: Raw sequence reads related to this manuscript have been deposited on NCBI under the BioProject 'RNAseq (10x and SMARTseq) of the tergal gland of Dalotia coriaria' (Accession: PRJNA707010; ID: 707010). All other data was uploaded to CaltechData: https://doi.org/10.22002/D1.1915 (processed scRNAseq 10x data), https://doi.org/10.22002/D1.1900 (processed SMARTseq data), https://doi.org/10.22002/D1.1905 (raw rheology video data), https://doi.org/10.22002/D1.1914 (transcriptome data), https://doi.org/10.22002/D1.1917 (RNAi experiments, survival assays, in vitro enzyme data), and https://doi.org/10.22002/D1.1916 (alignment and tree fasta files).\n\nCode availability: Detailed code for scRNAseq analyses with Seurat and cNMF; video analyses of rheology data; custom R scripts for SMARTseq analyses via sleuth, GOterm assignments and survival data analysis can be found on CaltechData (https://doi.org/10.22002/D1.1918). All other statistical comparisons using ANOVAs, Kruskal-Wallis tests, U-tests and simple ordinations were done in Past 3.04 (Hammer et al., 2001).\n\nPublished - 2021.05.13.444042v1.full.pdf
Supplemental Material - media-1.docx
", "abstract": "A long-standing challenge in biology is explaining how the functions of multicellular organs emerge from the underlying evolution of cell types. We deconstructed evolution of an organ novelty: a rove beetle gland that secretes a defensive cocktail. We show that gland function was pieced together via assembly of two cell types that manufacture distinct compounds. One cell type forms a chemical reservoir in the beetle's abdomen and produces alkane and ester compounds. We demonstrate that this cell type is a hybrid of cuticle cells and ancient pheromone and adipocyte-like cells, and executes its function via a mosaic of enzymes sourced from each parental cell type. The second cell type synthesizes noxious benzoquinones using a chimeric pathway derived from conserved cellular energy and cuticle formation pathways. We present evidence that evolution of each cell type was shaped by coevolution between the two cell types: the benzoquinones produced by the second cell type dissolve in solvents produced by the first, yielding a potent secretion that confers adaptive value onto the gland as a whole. Our findings illustrate how cooperation between cell types can arise, generating new, organ-level behaviors.", "date": "2021-05-15", "date_type": "published", "publisher": "bioRxiv", "id_number": "CaltechAUTHORS:20211217-183447306", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211217-183447306", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Rita Allen Foundation Scholars Award" }, { "agency": "Alfred P. Sloan Research Fellowship" }, { "agency": "Shurl and Kay Curci Foundation" }, { "agency": "Klingenstein-Simons Fellowship Award" }, { "agency": "NSF CAREER Award", "grant_number": "2047472" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2021.05.13.444042", "primary_object": { "basename": "2021.05.13.444042v1.full.pdf", "url": "https://authors.library.caltech.edu/records/24wrg-rx971/files/2021.05.13.444042v1.full.pdf" }, "related_objects": [ { "basename": "media-1.docx", "url": "https://authors.library.caltech.edu/records/24wrg-rx971/files/media-1.docx" } ], "resource_type": "monograph", "pub_year": "2021", "author_list": "Br\u00fcckner, Adrian; Badroos, Jean M.; et el." }, { "id": "https://authors.library.caltech.edu/records/sr5bw-wf220", "eprint_id": 90542, "eprint_status": "archive", "datestamp": "2023-08-19 05:32:50", "lastmod": "2023-10-18 23:31:01", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Parker-J", "name": { "family": "Parker", "given": "Joseph" }, "orcid": "0000-0001-9598-2454" }, { "id": "Eldredge-K-T", "name": { "family": "Eldredge", "given": "K. Taro" } }, { "id": "Thomas-I-M", "name": { "family": "Thomas", "given": "Isaiah M." } }, { "id": "Coleman-R", "name": { "family": "Coleman", "given": "Rory" } }, { "id": "Davis-S-R", "name": { "family": "Davis", "given": "Steven R." } } ] }, "title": "Hox-logic of body plan innovations for social symbiosis in rove beetles", "ispublished": "unpub", "full_text_status": "public", "keywords": "Hox genes, evolution, preadaptations, convergence, symbiosis", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. \n\nbioRxiv preprint first posted online Oct. 5, 2017. \n\nWe thank Brian Spencer (Applied Bionomics, Canada) for providing Dalotia, and Raymond Cloyd (Kansas State University), Graeme Murphy (Ontario Ministry of Food and Agriculture) and Richard Greatrex (Syngenta Bioline, UK) for advice on rearing this species. Yoshinori Tomoyasu provided important feedback on the manuscript. We are grateful to Gary Struhl (Columbia University) in whose laboratory part of this work was carried out. \n\nWe declare no competing interests.\n\nSubmitted - 198945.full.pdf
", "abstract": "How symbiotic lifestyles evolve from free-living ecologies is poorly understood. In Metazoa's largest family, Staphylinidae (rove beetles), numerous lineages have evolved obligate behavioral symbioses with ants or termites. Widespread convergence of this lifestyle is thought to stem from a novel, chemically defended body plan that enables free-living species to infiltrate colonies and undergo extreme evolutionary specialization. Here we show how this innovative body plan evolved, via new Hox functions in staphylinids that remodeled the coleopteran groundplan. Using a model staphylinid, Dalotia coriaria, we reveal the Hox basis for changes in thoracic appendage morphology that shortened the beetle elytron and left the abdomen physically unprotected, selecting for an abdominal defense gland that was likely key to unlocking ant and termite societies. We present evidence that the gland evolved through a novel, combinatorial role of the abdominal Hox proteins AbdA and AbdB. These proteins function together to specify distinct gland cell types in neighboring segmental compartments, each cell type synthesizing a different class of compound - irritant, ester and solvent. Only when secreted together do these compounds constitute a bioactive secretion, providing an example of emergent chemical functionality that arises from synergy between individual gland cell types. Hox-controlled specification of glandular diversity implies a modularity in compound biosynthesis that likely catalyzed the evolvability of rove beetle chemistry, including the capacity of symbiotic taxa to produce potent compounds for host deception. This study reveals how Hox-controlled body axis modifications predispose a major animal to convergently evolve into symbionts.", "date": "2018-11-01", "date_type": "published", "id_number": "CaltechAUTHORS:20181031-101742480", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181031-101742480", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1101/198945", "primary_object": { "basename": "198945.full.pdf", "url": "https://authors.library.caltech.edu/records/sr5bw-wf220/files/198945.full.pdf" }, "resource_type": "monograph", "pub_year": "2018", "author_list": "Parker, Joseph; Eldredge, K. Taro; et el." }, { "id": "https://authors.library.caltech.edu/records/4x1mf-a0v91", "eprint_id": 84319, "eprint_status": "archive", "datestamp": "2023-08-19 05:32:40", "lastmod": "2023-10-18 16:06:52", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Parker-J", "name": { "family": "Parker", "given": "Joseph" }, "orcid": "0000-0001-9598-2454" }, { "id": "Eldredge-K-T", "name": { "family": "Eldredge", "given": "K. Taro" } }, { "id": "Thomas-I-M", "name": { "family": "Thomas", "given": "Isaiah M." } }, { "id": "Coleman-R", "name": { "family": "Coleman", "given": "Rory" } }, { "id": "Davis-S-R", "name": { "family": "Davis", "given": "Steven R." } } ] }, "title": "Hox-logic of preadaptations for social insect symbiosis in rove beetles", "ispublished": "unpub", "full_text_status": "public", "keywords": "Hox genes, evolution, development, preadaptations, rove beetles, symbiosis", "note": "The copyright holder for this preprint is the author/funder. \n\nWe thank Brian Spencer (Applied Bionomics, Canada) for providing Dalotia, and Raymond Cloyd (Kansas State University), Graeme Murphy (Ontario Ministry of Food and Agriculture) and Richard Greatrex (Syngenta Bioline, UK) for advice on rearing this species. We are grateful to Gary Struhl (Columbia University) in whose laboratory part of this work was carried out.\n\nSubmitted - 198945.full.pdf
", "abstract": "How symbiotic lifestyles evolve from free-living ecologies is poorly understood. Novel traits mediating symbioses may stem from preadaptations: features of free-living ancestors that predispose taxa to engage in nascent interspecies relationships. In Metazoa's largest family, Staphylinidae (rove beetles), the body plan within the subfamily Aleocharinae is preadaptive for symbioses with social insects. Short elytra expose a pliable abdomen that bears targetable glands for host manipulation or chemical defense. The exposed abdomen has also been convergently refashioned into ant- and termite-mimicking shapes in multiple symbiotic lineages. Here we show how this preadaptive anatomy evolved via novel Hox gene functions that remodeled the ancestral coleopteran groundplan. Using the model staphylinid Dalotia coriaria, we abolished activities of the five thoracic and abdominal Hox genes. We show that elytral shortening is a staphylinid-specific property of the Hox-less appendage ground state, which is overridden in the metathorax by Ultrabithorax to promote hind wing expansion. In the exposed abdomen, we present evidence that defensive gland development stems from novel combinatorial outputs of the Abdominal-A and Abdominal-B Hox proteins: in the posterior compartment of tergite VI they specify a chemical gland reservoir, an imaginal disc-like invagination of ectodermal secretory cells; in the anterior compartment of tergite VII Abdominal-A and Abdominal-B specify clusters of classical duct-bearing glands. These distinct gland cell types collectively synthesize a blend of benzoquinone irritants, surfactant esters and alkane solvent, a defensive chemistry, which in symbiotic species has been augmented with specialized volatiles that potently manipulate ant behavior. These results reveal how Hox-controlled body axis modifications caused a convergent trend towards evolving symbiosis in the Metazoa.", "date": "2018-01-16", "date_type": "published", "id_number": "CaltechAUTHORS:20180112-141851988", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180112-141851988", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1101/198945", "primary_object": { "basename": "198945.full.pdf", "url": "https://authors.library.caltech.edu/records/4x1mf-a0v91/files/198945.full.pdf" }, "resource_type": "monograph", "pub_year": "2018", "author_list": "Parker, Joseph; Eldredge, K. Taro; et el." } ]