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Pavón-Vázquez CJ, Rana Q, Farleigh K, Crispo E, Zeng M, Liliah J, Mulcahy D, Ascanio A, Jezkova T, Leaché AD, Flouri T, Yang Z, Blair C. Gene Flow and Isolation in the Arid Nearctic Revealed by Genomic Analyses of Desert Spiny Lizards. Syst Biol 2024; 73:323-342. [PMID: 38190300 DOI: 10.1093/sysbio/syae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 12/18/2023] [Accepted: 01/05/2024] [Indexed: 01/10/2024] Open
Abstract
The opposing forces of gene flow and isolation are two major processes shaping genetic diversity. Understanding how these vary across space and time is necessary to identify the environmental features that promote diversification. The detection of considerable geographic structure in taxa from the arid Nearctic has prompted research into the drivers of isolation in the region. Several geographic features have been proposed as barriers to gene flow, including the Colorado River, Western Continental Divide (WCD), and a hypothetical Mid-Peninsular Seaway in Baja California. However, recent studies suggest that the role of barriers in genetic differentiation may have been overestimated when compared to other mechanisms of divergence. In this study, we infer historical and spatial patterns of connectivity and isolation in Desert Spiny Lizards (Sceloporus magister) and Baja Spiny Lizards (Sceloporus zosteromus), which together form a species complex composed of parapatric lineages with wide distributions in arid western North America. Our analyses incorporate mitochondrial sequences, genomic-scale data, and past and present climatic data to evaluate the nature and strength of barriers to gene flow in the region. Our approach relies on estimates of migration under the multispecies coalescent to understand the history of lineage divergence in the face of gene flow. Results show that the S. magister complex is geographically structured, but we also detect instances of gene flow. The WCD is a strong barrier to gene flow, while the Colorado River is more permeable. Analyses yield conflicting results for the catalyst of differentiation of peninsular lineages in S. zosteromus. Our study shows how large-scale genomic data for thoroughly sampled species can shed new light on biogeography. Furthermore, our approach highlights the need for the combined analysis of multiple sources of evidence to adequately characterize the drivers of divergence.
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Affiliation(s)
- Carlos J Pavón-Vázquez
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY 11201, USA
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Colonia Los Reyes Ixtacala, Tlalnepantla, Estado de México, C.P. 54090, México
| | - Qaantah Rana
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY 11201, USA
| | - Keaka Farleigh
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Erika Crispo
- Department of Biology, Pace University, One Pace Plaza, New York, NY 10038, USA
| | - Mimi Zeng
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY 11201, USA
| | - Jeevanie Liliah
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY 11201, USA
| | - Daniel Mulcahy
- Collection Future, Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin 10115, Germany
| | - Alfredo Ascanio
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Tereza Jezkova
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98195, USA
| | - Tomas Flouri
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Christopher Blair
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY 11201, USA
- Biology PhD Program, CUNY Graduate Center, 365 5th Ave., New York, NY 10016, USA
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Kulkarni SS, Steiner HG, Garcia EL, Iuri H, Jones RR, Ballesteros JA, Gainett G, Graham MR, Harms D, Lyle R, Ojanguren-Affilastro AA, Santibañez-López CE, Silva de Miranda G, Cushing PE, Gavish-Regev E, Sharma PP. Neglected no longer: Phylogenomic resolution of higher-level relationships in Solifugae. iScience 2023; 26:107684. [PMID: 37694155 PMCID: PMC10484990 DOI: 10.1016/j.isci.2023.107684] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/26/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023] Open
Abstract
Advanced sequencing technologies have expedited resolution of higher-level arthropod relationships. Yet, dark branches persist, principally among groups occurring in cryptic habitats. Among chelicerates, Solifugae ("camel spiders") is the last order lacking a higher-level phylogeny and have thus been historically characterized as "neglected [arachnid] cousins". Though renowned for aggression, remarkable running speed, and xeric adaptation, inferring solifuge relationships has been hindered by inaccessibility of diagnostic morphological characters, whereas molecular investigations have been limited to one of 12 recognized families. Our phylogenomic dataset via capture of ultraconserved elements sampling all extant families recovered a well-resolved phylogeny, with two distinct groups of New World taxa nested within a broader Paleotropical radiation. Divergence times using fossil calibrations inferred that Solifugae radiated by the Permian, and most families diverged prior to the Paleogene-Cretaceous extinction, likely driven by continental breakup. We establish Boreosolifugae new suborder uniting five Laurasian families, and Australosolifugae new suborder uniting seven Gondwanan families using morphological and biogeographic signal.
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Affiliation(s)
- Siddharth S. Kulkarni
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Hugh G. Steiner
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Erika L. Garcia
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO 80205, USA
| | - Hernán Iuri
- División de Aracnología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Buenos Aires 1405DJR, Argentina
| | - R. Ryan Jones
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO 80205, USA
| | | | - Guilherme Gainett
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Matthew R. Graham
- Department of Biology, Eastern Connecticut State University, Willimantic, CT 06226, USA
| | - Danilo Harms
- Museum of Nature Hamburg - Zoology, Department of Invertebrates, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg, Germany
| | - Robin Lyle
- Biosystematics: Arachnology, ARC—Plant Health and Protection, Pretoria, South Africa
| | | | | | - Gustavo Silva de Miranda
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Paula E. Cushing
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO 80205, USA
| | - Efrat Gavish-Regev
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Prashant P. Sharma
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI 53706, USA
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Green TA, Hutchings PA, Scarff FR, Tweedley JR, Calver MC. Research publications of Australia's natural history museums, 1981-2020: Enduring relevance in a changing world. PLoS One 2023; 18:e0287659. [PMID: 37352318 PMCID: PMC10289469 DOI: 10.1371/journal.pone.0287659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 06/12/2023] [Indexed: 06/25/2023] Open
Abstract
As a case study of the responses of natural history museums to changing scientific and funding environments, we analysed research publications of Australia's Natural History Museums (ANHMs) 1981-2020. Using Scopus, 9,923 relevant documents 1981-2020 were identified, mainly research papers but with a growing proportion of reviews. The number of documents published increased over tenfold from 39 (1981) to 553 (2020), likely driven by collaborations (rising from 28.5% of documents 1981-1985 to 87.2% of documents 2016-2020), contributions from retired staff, and volunteer support. The mean length of documents (pages) ranged from a low of 15.3 in 2001-2005 to a high of 17.4 in 1991-1995, but this statistically significant result was trivial in practical terms. The sources (i.e., journals, book titles, conference proceedings) in which ANHM authors published changed over time, with growing proportions of publications in journals covering molecular ecology/phylogenetics and biological conservation. We identified the major areas of study canvassed within the corpus of publications by developing structural topic models based on patterns of word use in document titles, abstracts and keyword lists. The topics discovered included study subjects traditional for natural history museums (new taxa, phylogeny, systematics, animal morphology, palaeontology, minerals), new directions (molecular genetics, ecology, biological conservation) and marine biology (probably reflecting Australia's large coastline). Most citations came from Australia, USA and UK, although in 2016-2020 only 27.9% of citing documents included an Australian author. Growth in numbers of documents and collaborations, as well as use of documents internationally over a period of great change in scientific and funding environments, indicate an enduring legacy of ANHM research, grounded on the intrinsic value of the collections.
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Affiliation(s)
- Tayla A. Green
- Environmental and Conservation Sciences, Murdoch University, Murdoch, Western Australia, Australia
| | - Pat A. Hutchings
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
- Department of Biological Sciences, Macquarie University, North Ryde, Australia
| | - Fiona R. Scarff
- Environmental and Conservation Sciences, Murdoch University, Murdoch, Western Australia, Australia
| | - James R. Tweedley
- Environmental and Conservation Sciences, Murdoch University, Murdoch, Western Australia, Australia
| | - Michael C. Calver
- Environmental and Conservation Sciences, Murdoch University, Murdoch, Western Australia, Australia
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Patterns in schizomid flagellum shape from elliptical Fourier analysis. Sci Rep 2022; 12:3896. [PMID: 35273227 PMCID: PMC8913634 DOI: 10.1038/s41598-022-07823-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/24/2022] [Indexed: 11/11/2022] Open
Abstract
The arachnid order Schizomida is a relatively understudied group of soil-dwelling predators found on all continents except Antarctica. While efforts to understand their biology are growing, there is still much to know about them. A curious aspect of their morphology is the male flagellum, a sexually dimorphic, tail-like structure which differs in shape across the order and functions in their courtship rituals. The flagellar shape is important for taxonomic classification, yet few efforts have been made to examine shape diversity across the group. Using elliptical Fourier analysis, a type of geometric morphometrics based on shape outline, we quantified shape differences across a combined nearly 550 outlines in the dorsal and lateral views, categorizing them based on genus, family, biogeographic realm, and habitat, with special emphasis on Caribbean and Cuban fauna. We tested for allometric relationships, differences in disparity based on locations and sizes in morphospace among these categories, and for clusters of shapes in morphospace. We found multiple differences in all categories despite apparent overlaps in morphospace, evolutionary allometry, and evidence for discrete clusters in some flagellum shapes. This study can serve as a foundation for further study on the evolution, diversification, and taxonomic utility of the male flagellum.
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