1
|
Nishida S, Takano A, Suyama Y, Kakishima S. Detection of reproductive interference between closely related Salvia species with small-scale separated distributions by multifaceted pollination and molecular analyses. JOURNAL OF PLANT RESEARCH 2024:10.1007/s10265-024-01577-6. [PMID: 39214907 DOI: 10.1007/s10265-024-01577-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Reproductive interference, an interspecific interaction in reproductive process that exerts an adverse effect, has gained attention as a contributing factor in promoting exclusive distributions between closely related species. However, detailed studies on the possibility of reproductive interference between native plants are still lacking, presumably because strong reproductive interference can rapidly realize exclusive distributions, leaving the two species apparently independent. Salvia japonica and S. lutescens are found in separate localities at a small scale, although their distributions overlap at a large scale. We investigated the possibility of reproductive interference between them through field surveys, hand-pollination experiments, evaluation of hybrid fertility, cpDNA and nrDNA genotyping, and genome-wide DNA analysis. The field survey results did not reveal apparent negative interaction in competition for pollinator services. Mixed pollination with conspecific pollen and counterpart pollen reduced seed set in S. japonica, and hybrid progeny produced by mixed pollination were less than 20% as fertile compared to the pure species. The DNA genotyping results suggested the possibility of hybridization where their distributions overlap, and the genome-wide DNA analysis results showed clear genetic differentiation between the two species as well as the existence of hybrids. These results suggest that bi-directional reproductive interference between S. japonica and S. lutescens may have led to their present separated distributions at a small scale.
Collapse
Affiliation(s)
- Sachiko Nishida
- Nagoya University Museum, Furo-Cho, Chikusa-Ku, Nagoya, 464-8601, Japan.
| | - Atsuko Takano
- University of Hyogo/ Museum of Nature and Human Activities, Yayoigaoka 6, Sanda, Hyogo, 669-1546, Japan
| | - Yoshihisa Suyama
- Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-Onsen, Osaki, Miyagi, 989-6711, Japan
| | - Satoshi Kakishima
- Department of Botany, National Museum of Nature and Science, 4-1-1, Amakubo, Tsukuba-Shi, Ibaraki, 305-0005, Japan
- The Mt. Fuji Institute for Nature and Biology, Showa University, 4562 Kamiyoshida, Fujiyoshida, Yamanashi, 403-0005, Japan
| |
Collapse
|
2
|
Rose JP, Kriebel R, Sytsma KJ, Drew BT. Phylogenomic perspectives on speciation and reproductive isolation in a North American biodiversity hotspot: an example using California sages (Salvia subgenus Audibertia: Lamiaceae). ANNALS OF BOTANY 2024; 134:295-310. [PMID: 38733329 PMCID: PMC11232522 DOI: 10.1093/aob/mcae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND AND AIMS The California Floristic Province (CA-FP) is the most species-rich region of North America north of Mexico. One of several proposed hypotheses explaining the exceptional diversity of the region is that the CA-FP harbours myriad recently diverged lineages with nascent reproductive barriers. Salvia subgenus Audibertia is a conspicuous element of the CA-FP, with multiple sympatric and compatible species. METHODS Using 305 nuclear loci and both organellar genomes, we reconstruct species trees, examine genomic discordance, conduct divergence-time estimation, and analyse contemporaneous patterns of gene flow and mechanical reproductive isolation. KEY RESULTS Despite strong genomic discordance, an underlying bifurcating tree is supported. Organellar genomes capture additional introgression events not detected in the nuclear genome. Most interfertility is found within clades, indicating that reproductive barriers arise with increasing genetic divergence. Species are generally not mechanically isolated, suggesting that it is unlikely to be the primary factor leading to reproductive isolation. CONCLUSIONS Rapid, recent speciation with some interspecific gene flow in conjunction with the onset of a Mediterranean-like climate is the underlying cause of extant diversity in Salvia subgenus Audibertia. Speciation has largely not been facilitated by gene flow. Its signal in the nuclear genome seems to mostly be erased by backcrossing, but organellar genomes each capture different instances of historical gene flow, probably characteristic of many CA-FP lineages. Mechanical reproductive isolation appears to be only part of a mosaic of factors limiting gene flow.
Collapse
Affiliation(s)
- Jeffrey P Rose
- Department of Biology, University of Nebraska at Kearney, Kearney, NE 68849, USA
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
- California Academy of Sciences, San Francisco, CA 94118, USA
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Bryan T Drew
- Department of Biology, University of Nebraska at Kearney, Kearney, NE 68849, USA
| |
Collapse
|
3
|
Gvoždík V, Dolinay M, Zassi-Boulou AG, Lemmon AR, Lemmon EM, Procházka M. Central African dwarf crocodiles found in syntopy are comparably divergent to South American dwarf caimans. Biol Lett 2024; 20:20230448. [PMID: 38716586 PMCID: PMC11135362 DOI: 10.1098/rsbl.2023.0448] [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: 09/25/2023] [Revised: 12/18/2023] [Accepted: 03/04/2024] [Indexed: 05/31/2024] Open
Abstract
Recent molecular taxonomic advancements have expanded our understanding of crocodylian diversity, revealing the existence of previously overlooked species, including the Congo dwarf crocodile (Osteolaemus osborni) in the central Congo Basin rainforests. This study explores the genomic divergence between O. osborni and its better-known relative, the true dwarf crocodile (Osteolaemus tetraspis), shedding light on their evolutionary history. Field research conducted in the northwestern Republic of the Congo uncovered a locality where both species coexist in sympatry/syntopy. Genomic analysis of sympatric individuals reveals a level of divergence comparable to that between ecologically similar South American dwarf caimans (Paleosuchus palpebrosus and Paleosuchus trigonatus), suggesting parallel speciation in the Afrotropics and Neotropics during the Middle to Late Miocene, 10-12 Ma. Comparison of the sympatric and allopatric dwarf crocodiles indicates no gene flow between the analysed sympatric individuals of O. osborni and O. tetraspis. However, a larger sample will be required to answer the question of whether or to what extent these species hybridize. This study emphasizes the need for further research on the biology and conservation status of the Congo dwarf crocodile, highlighting its significance in the unique biodiversity of the Congolian rainforests and thus its potential as a flagship species.
Collapse
Affiliation(s)
- Václav Gvoždík
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Zoology, National Museum of the Czech Republic, Prague, Czech Republic
| | - Matej Dolinay
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Ange-Ghislain Zassi-Boulou
- Department of Biology, National Institute for Research in Exact and Natural Sciences (IRSEN), Brazzaville, Republic of the Congo
| | - Alan R. Lemmon
- Department of Scientific Computing, Dirac Science Library, Florida State University, Tallahassee, FL, USA
| | - Emily M. Lemmon
- Department of Biological Sciences, Florida State University, Tallahassee, FL, USA
| | | |
Collapse
|
4
|
Opatova V, Bourguignon K, Bond JE. Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae). Mol Ecol Resour 2024; 24:e13894. [PMID: 37971187 DOI: 10.1111/1755-0998.13894] [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: 07/04/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
The outcome of species delimitation depends on many factors, including conceptual framework, study design, data availability, methodology employed and subjective decision making. Obtaining sufficient taxon sampling in endangered or rare taxa might be difficult, particularly when non-lethal tissue collection cannot be utilized. The need to avoid overexploitation of the natural populations may thus limit methodological framework available for downstream data analyses and bias the results. We test species boundaries in rare North American trapdoor spider genus Cyclocosmia Ausserer (1871) inhabiting the Southern Coastal Plain biodiversity hotspot with the use of genomic data and two multispecies coalescent model methods. We evaluate the performance of each methodology within a limited sampling framework. To mitigate the risk of species over splitting, common in taxa with highly structured populations, we subsequently implement a species validation step via genealogical diversification index (gdi), which accounts for both genetic isolation and gene flow. We delimited eight geographically restricted lineages within sampled North American Cyclocosmia, suggesting that major river drainages in the region are likely barriers to dispersal. Our results suggest that utilizing BPP in the species discovery step might be a good option for datasets comprising hundreds of loci, but fewer individuals, which may be a common scenario for rare taxa. However, we also show that such results should be validated via gdi, in order to avoid over splitting.
Collapse
Affiliation(s)
- Vera Opatova
- Department of Zoology, Faculty of Sciences, Charles University, Prague 2, Czech Republic
| | - Kellie Bourguignon
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Jason E Bond
- Department of Entomology and Nematology, University of California, Davis, California, USA
| |
Collapse
|
5
|
Karimi N, Krieg CP, Spalink D, Lemmon AR, Lemmon EM, Eifler E, Hernández AI, Chan PW, Rodríguez A, Landis JB, Strickler SR, Specht CD, Givnish TJ. Chromosomal evolution, environmental heterogeneity, and migration drive spatial patterns of species richness in Calochortus (Liliaceae). Proc Natl Acad Sci U S A 2024; 121:e2305228121. [PMID: 38394215 PMCID: PMC10927571 DOI: 10.1073/pnas.2305228121] [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: 03/31/2023] [Accepted: 12/20/2023] [Indexed: 02/25/2024] Open
Abstract
We used nuclear genomic data and statistical models to evaluate the ecological and evolutionary processes shaping spatial variation in species richness in Calochortus (Liliaceae, 74 spp.). Calochortus occupies diverse habitats in the western United States and Mexico and has a center of diversity in the California Floristic Province, marked by multiple orogenies, winter rainfall, and highly divergent climates and substrates (including serpentine). We used sequences of 294 low-copy nuclear loci to produce a time-calibrated phylogeny, estimate historical biogeography, and test hypotheses regarding drivers of present-day spatial patterns in species number. Speciation and species coexistence require reproductive isolation and ecological divergence, so we examined the roles of chromosome number, environmental heterogeneity, and migration in shaping local species richness. Six major clades-inhabiting different geographic/climatic areas, and often marked by different base chromosome numbers (n = 6 to 10)-began diverging from each other ~10.3 Mya. As predicted, local species number increased significantly with local heterogeneity in chromosome number, elevation, soil characteristics, and serpentine presence. Species richness is greatest in the Transverse/Peninsular Ranges where clades with different chromosome numbers overlap, topographic complexity provides diverse conditions over short distances, and several physiographic provinces meet allowing immigration by several clades. Recently diverged sister-species pairs generally have peri-patric distributions, and maximum geographic overlap between species increases over the first million years since divergence, suggesting that chromosomal evolution, genetic divergence leading to gametic isolation or hybrid inviability/sterility, and/or ecological divergence over small spatial scales may permit species co-occurrence.
Collapse
Affiliation(s)
- Nisa Karimi
- Science and Conservation Division, Missouri Botanical Garden, St. Louis, MO63110
- Department of Botany, University of Wisconsin-Madison, Madison, WI53706
| | | | - Daniel Spalink
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX77845
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL32306
| | | | - Evan Eifler
- Department of Botany, University of Wisconsin-Madison, Madison, WI53706
| | - Adriana I. Hernández
- School of Integrative Plant Science, Cornell University, Ithaca, NY14853
- L. H. Bailey Hortorium, Cornell University, Ithaca, NY14853
| | - Patricia W. Chan
- Department of Botany, University of Wisconsin-Madison, Madison, WI53706
| | - Aarón Rodríguez
- Departamento de Botánica y Zoología, Universidad de la Guadalajara, Zapopan, Jalisco45200, Mexico
| | - Jacob B. Landis
- School of Integrative Plant Science, Cornell University, Ithaca, NY14853
- Departamento de Botánica y Zoología, Universidad de la Guadalajara, Zapopan, Jalisco45200, Mexico
- Boyce Thompson Institute for Plant Research, Ithaca, NY14853
| | | | - Chelsea D. Specht
- School of Integrative Plant Science, Cornell University, Ithaca, NY14853
- L. H. Bailey Hortorium, Cornell University, Ithaca, NY14853
| | - Thomas J. Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, WI53706
| |
Collapse
|
6
|
Kulkarni S, Wood HM, Hormiga G. Advances in the reconstruction of the spider tree of life: A roadmap for spider systematics and comparative studies. Cladistics 2023; 39:479-532. [PMID: 37787157 DOI: 10.1111/cla.12557] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 07/27/2023] [Accepted: 08/17/2023] [Indexed: 10/04/2023] Open
Abstract
In the last decade and a half, advances in genetic sequencing technologies have revolutionized systematics, transforming the field from studying morphological characters or a few genetic markers, to genomic datasets in the phylogenomic era. A plethora of molecular phylogenetic studies on many taxonomic groups have come about, converging on, or refuting prevailing morphology or legacy-marker-based hypotheses about evolutionary affinities. Spider systematics has been no exception to this transformation and the inter-relationships of several groups have now been studied using genomic data. About 51 500 extant spider species have been described, all with a conservative body plan, but innumerable morphological and behavioural peculiarities. Inferring the spider tree of life using morphological data has been a challenging task. Molecular data have corroborated many hypotheses of higher-level relationships, but also resulted in new groups that refute previous hypotheses. In this review, we discuss recent advances in the reconstruction of the spider tree of life and highlight areas where additional effort is needed with potential solutions. We base this review on the most comprehensive spider phylogeny to date, representing 131 of the 132 spider families. To achieve this sampling, we combined six Sanger-based markers with newly generated and publicly available genome-scale datasets. We find that some inferred relationships between major lineages of spiders (such as Austrochiloidea, Palpimanoidea and Synspermiata) are robust across different classes of data. However, several new hypotheses have emerged with different classes of molecular data. We identify and discuss the robust and controversial hypotheses and compile this blueprint to design future studies targeting systematic revisions of these problematic groups. We offer an evolutionary framework to explore comparative questions such as evolution of venoms, silk, webs, morphological traits and reproductive strategies.
Collapse
Affiliation(s)
- Siddharth Kulkarni
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC, 20560, USA
| | - Hannah M Wood
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 1000 Constitution Avenue NW, Washington, DC, 20560, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA
| |
Collapse
|
7
|
Li YD, Engel MS, Tihelka E, Cai C. Phylogenomics of weevils revisited: data curation and modelling compositional heterogeneity. Biol Lett 2023; 19:20230307. [PMID: 37727076 PMCID: PMC10509570 DOI: 10.1098/rsbl.2023.0307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023] Open
Abstract
Weevils represent one of the most prolific radiations of beetles and the most diverse group of herbivores on land. The phylogeny of weevils (Curculionoidea) has received extensive attention, and a largely satisfactory framework for their interfamilial relationships has been established. However, a recent phylogenomic study of Curculionoidea based on anchored hybrid enrichment (AHE) data yielded an abnormal placement for the family Belidae (strongly supported as sister to Nemonychidae + Anthribidae). Here we reanalyse the genome-scale AHE data for Curculionoidea using various models of molecular evolution and data filtering methods to mitigate anticipated systematic errors and reduce compositional heterogeneity. When analysed with the infinite mixture model CAT-GTR or using appropriately filtered datasets, Belidae are always recovered as sister to the clade (Attelabidae, (Caridae, (Brentidae, Curculionidae))), which is congruent with studies based on morphology and other sources of molecular data. Although the relationships of the 'higher Curculionidae' remain challenging to resolve, we provide a consistent and robust backbone phylogeny of weevils. Our extensive analyses emphasize the significance of data curation and modelling across-site compositional heterogeneity in phylogenomic studies.
Collapse
Affiliation(s)
- Yan-Da Li
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Michael S. Engel
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024-5192, USA
| | - Erik Tihelka
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Chenyang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| |
Collapse
|
8
|
Forthman M, Gordon ERL, Kimball RT. Low hybridization temperatures improve target capture success of invertebrate loci: a case study of leaf-footed bugs (Hemiptera: Coreoidea). ROYAL SOCIETY OPEN SCIENCE 2023; 10:230307. [PMID: 37388308 PMCID: PMC10300676 DOI: 10.1098/rsos.230307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/12/2023] [Indexed: 07/01/2023]
Abstract
Target capture is widely used in phylogenomic, ecological and functional genomic studies. Bait sets that allow capture from a diversity of species can be advantageous, but high-sequence divergence from baits can limit yields. Currently, only four experimental comparisons of a critical target capture parameter, hybridization temperature, have been published. These have been in vertebrates, where bait divergences are typically low, and none include invertebrates where bait-target divergences may be higher. Most invertebrate capture studies use a fixed, high hybridization temperature to maximize the proportion of on-target data, but many report low locus recovery. Using leaf-footed bugs (Hemiptera: Coreoidea), we investigate the effect of hybridization temperature on capture success of ultraconserved elements targeted by (i) baits developed from divergent hemipteran genomes and (ii) baits developed from less divergent coreoid transcriptomes. Lower temperatures generally resulted in more contigs and improved recovery of targets despite a lower proportion of on-target reads, lower read depth and more putative paralogues. Hybridization temperatures had less of an effect when using transcriptome-derived baits, which is probably due to lower bait-target divergences and greater bait tiling density. Thus, accommodating low hybridization temperatures during target capture can provide a cost-effective, widely applicable solution to improve invertebrate locus recovery.
Collapse
Affiliation(s)
- Michael Forthman
- California State Collection of Arthropods, Plant Pest Diagnostics Branch, California Department of Food and Agriculture, 3294 Meadowview Road, Sacramento, CA 95832, USA
- Entomology and Nematology Department, University of Florida, 1881 Natural Area Drive, Gainesville, FL 32611, USA
| | - Eric R. L. Gordon
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75N. Eagleville Road, Unit 3043, Storrs, CT 06269, USA
| | - Rebecca T. Kimball
- Department of Biology, University of Florida, 876 Newell Drive, Gainesville, FL 32611, USA
| |
Collapse
|
9
|
Zhang J, Li Z, Lai J, Zhang Z, Zhang F. A novel probe set for the phylogenomics and evolution of RTA spiders. Cladistics 2023; 39:116-128. [PMID: 36719825 DOI: 10.1111/cla.12523] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/10/2022] [Accepted: 12/21/2022] [Indexed: 02/01/2023] Open
Abstract
Spiders are important models for evolutionary studies of web building, sexual selection and adaptive radiation. The recent development of probes for UCE (ultra-conserved element)-based phylogenomic studies has shed light on the phylogeny and evolution of spiders. However, the two available UCE probe sets for spider phylogenomics (Spider and Arachnida probe sets) have relatively low capture efficiency within spiders, and are not optimized for the retrolateral tibial apophysis (RTA) clade, a hyperdiverse lineage that is key to understanding the evolution and diversification of spiders. In this study, we sequenced 15 genomes of species in the RTA clade, and using eight reference genomes, we developed a new UCE probe set (41 845 probes targeting 3802 loci, labelled as the RTA probe set). The performance of the RTA probes in resolving the phylogeny of the RTA clade was compared with the Spider and Arachnida probes through an in-silico test on 19 genomes. We also tested the new probe set empirically on 28 spider species of major spider lineages. The results showed that the RTA probes recovered twice and four times as many loci as the other two probe sets, and the phylogeny from the RTA UCEs provided higher support for certain relationships. This newly developed UCE probe set shows higher capture efficiency empirically and is particularly advantageous for phylogenomic and evolutionary studies of RTA clade and jumping spiders.
Collapse
Affiliation(s)
- Junxia Zhang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Zhaoyi Li
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Jiaxing Lai
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Zhisheng Zhang
- School of Life Sciences, Southwest University, Chongqing, 400700, China
| | - Feng Zhang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| |
Collapse
|
10
|
Benítez-Villaseñor A, Granados Mendoza C, Wanke S, Peñafiel Cevallos M, Freire ME, Lemmon EM, Lemmon AR, Magallón S. The use of Anchored Hybrid Enrichment data to resolve higher-level phylogenetic relationships: A proof-of-concept applied to Asterales (Eudicotyledoneae; Angiosperms). Mol Phylogenet Evol 2023; 181:107714. [PMID: 36708940 DOI: 10.1016/j.ympev.2023.107714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 10/28/2022] [Accepted: 01/18/2023] [Indexed: 01/26/2023]
Abstract
Anchored Hybrid Enrichment (AHE) is a tool for capturing orthologous regions of the nuclear genome shared in low or single copy across lineages. Despite the increasing number of studies using this method, its usefulness to estimate relationships at deeper taxonomic levels in plants has not been fully explored. Here we present a proof of concept about the performance of nuclear loci obtained with AHE to infer phylogenetic relationships and explore the use of gene sampling schemes to estimate divergence times in Asterales. We recovered low-copy nuclear loci using the AHE method from herbarium material and silica-preserved samples. Maximum likelihood, Bayesian inference, and coalescence approaches were used to reconstruct phylogenomic relationships. Dating analyses were conducted under a multispecies coalescent approach by jointly inferring species tree and divergence times with random gene sampling schemes and multiple calibrations. We recovered 403 low-copy nuclear loci for 63 species representing nine out of eleven families of Asterales. Phylogenetic hypotheses were congruent among the applied methods and previously published results. Analyses with concatenated datasets were strongly supported, but coalescence-based analyses showed low support for the phylogenetic position of families Argophyllaceae and Alseuosmiaceae. Estimated family ages were congruent among gene sampling schemes, with the mean age for Asterales around 130 Myr. Our study documents the usefulness of AHE for resolving phylogenetic relationships at deep phylogenetic levels in Asterales. Observed phylogenetic inconsistencies were possibly due to the non-inclusion of families Phellinceae and Pentaphragmataceae. Random gene sampling schemes produced consistent age estimates with coalescence and species tree relaxed clock approaches.
Collapse
Affiliation(s)
- Adriana Benítez-Villaseñor
- Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, A. P. 70-153, C.P.04510 Ciudad de México, Mexico.
| | - Carolina Granados Mendoza
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico; Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20, 01217 Dresden, Germany.
| | - Stefan Wanke
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico; Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20, 01217 Dresden, Germany.
| | - Marcia Peñafiel Cevallos
- Herbario Nacional del Ecuador (QCNE), Instituto Nacional de Biodiversidad, Quito 170135, Ecuador.
| | - M Efraín Freire
- Herbario Nacional del Ecuador (QCNE), Instituto Nacional de Biodiversidad, Quito 170135, Ecuador.
| | - Emily Moriarty Lemmon
- Department of Biology, Florida State University 319 Stadium Drive, P.O. Box 3064295, Tallahassee, FL 32306-4295, United States.
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University 400 Dirac Science Library, Tallahassee, FL 32306-4120, United States.
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico.
| |
Collapse
|
11
|
Nunes R, Storer C, Doleck T, Kawahara AY, Pierce NE, Lohman DJ. Predictors of sequence capture in a large-scale anchored phylogenomics project. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.943361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
Next-generation sequencing (NGS) technologies have revolutionized phylogenomics by decreasing the cost and time required to generate sequence data from multiple markers or whole genomes. Further, the fragmented DNA of biological specimens collected decades ago can be sequenced with NGS, reducing the need for collecting fresh specimens. Sequence capture, also known as anchored hybrid enrichment, is a method to produce reduced representation libraries for NGS sequencing. The technique uses single-stranded oligonucleotide probes that hybridize with pre-selected regions of the genome that are sequenced via NGS, culminating in a dataset of numerous orthologous loci from multiple taxa. Phylogenetic analyses using these sequences have the potential to resolve deep and shallow phylogenetic relationships. Identifying the factors that affect sequence capture success could save time, money, and valuable specimens that might be destructively sampled despite low likelihood of sequencing success. We investigated the impacts of specimen age, preservation method, and DNA concentration on sequence capture (number of captured sequences and sequence quality) while accounting for taxonomy and extracted tissue type in a large-scale butterfly phylogenomics project. This project used two probe sets to extract 391 loci or a subset of 13 loci from over 6,000 butterfly specimens. We found that sequence capture is a resilient method capable of amplifying loci in samples of varying age (0–111 years), preservation method (alcohol, papered, pinned), and DNA concentration (0.020 ng/μl - 316 ng/ul). Regression analyses demonstrate that sequence capture is positively correlated with DNA concentration. However, sequence capture and DNA concentration are negatively correlated with sample age and preservation method. Our findings suggest that sequence capture projects should prioritize the use of alcohol-preserved samples younger than 20 years old when available. In the absence of such specimens, dried samples of any age can yield sequence data, albeit with returns that diminish with increasing age.
Collapse
|
12
|
Stout C, Schonhuth S, Mayden R, Garrison NL, Armbruster JW. Phylogenomics and classification of Notropis and related shiners (Cypriniformes: Leuciscidae) and the utility of exon capture on lower taxonomic groups. PeerJ 2022; 10:e14072. [PMID: 36248715 PMCID: PMC9558623 DOI: 10.7717/peerj.14072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/27/2022] [Indexed: 01/20/2023] Open
Abstract
North American minnows of the Shiner Clade, within the family Leuciscidae, represent one of the most taxonomically complex clades of the order Cypriniformes due to the large number of taxa coupled with conserved morphologies. Species within this clade were moved between genera and subgenera until the community decided to lump many of the unclassified taxa with similar morphologies into one genus, Notropis, which has held up to 325 species. Despite phylogentic studies that began to re-elevate some genera merged into Notropis, such as Cyprinella, Luxilus, Lythrurus, and Pteronotropis, the large genus Notropis remained as a taxonomic repository for many shiners of uncertain placement. Recent molecular advances in sequencing technologies have provided the opportunity to re-examine the Shiner Clade using phylogenomic markers. Using a fish probe kit, we sequenced 90 specimens in 87 species representing 16 genera included in the Shiner Clade, with a resulting dataset of 1,004 loci and 286,455 base pairs. Despite the large dataset, only 32,349 bp (11.29%) were phylogenetically informative. In our maximum likelihood tree, 78% of nodes are 100% bootstrap supported demonstrating the utility of the phylogenomic markers at lower taxonomic levels. Unsurprisingly, species within Notropis as well as Hudsonius, Luxilus, and Alburnops are not resolved as monophyletic groups. Cyprinella is monophyletic if Cyprinella callistia is excluded, and Pteronotropis is monophyletic if it includes Hudsonius cummingsae. Taxonomic changes we propose are: restriction of species included in Alburnops and Notropis, elevation of the subgenus Hydrophlox, expansion of species included in Miniellus, movement of Hudsonius cummingsae to Pteronotropis, and resurrection of the genera Coccotis and Paranotropis. We additionally had two specimens of three species, Notropis atherinoides, Ericymba amplamala, and Pimephales vigilax and found signficant differences between the localities (1,086, 1,424, and 845 nucleotides respectively).
Collapse
Affiliation(s)
- Carla Stout
- Department of Biological Sciences, California State Polytechnic University, Pomona, Pomona, CA, United States of America
| | - Susana Schonhuth
- Department of Biology, Saint Louis University, St. Louis, MO, United States of America
| | - Richard Mayden
- Department of Biology, Saint Louis University, St. Louis, MO, United States of America
| | - Nicole L. Garrison
- Department of Biology, West Liberty University, West Liberty, WV, United States of America
| | - Jonathan W. Armbruster
- Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
| |
Collapse
|
13
|
A strong backbone for an invertebrate group: anchored phylogenomics improves the resolution of genus-level relationships within the Lumbricidae (Annelida, Crassiclitellata). ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00570-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
|
14
|
Singh P, Irisarri I, Torres‐Dowdall J, Thallinger GG, Svardal H, Lemmon EM, Lemmon AR, Koblmüller S, Meyer A, Sturmbauer C. Phylogenomics of trophically diverse cichlids disentangles processes driving adaptive radiation and repeated trophic transitions. Ecol Evol 2022; 12:e9077. [PMID: 35866021 PMCID: PMC9288888 DOI: 10.1002/ece3.9077] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/28/2022] [Accepted: 05/31/2022] [Indexed: 11/12/2022] Open
Abstract
Cichlid fishes of the tribe Tropheini are a striking case of adaptive radiation, exemplifying multiple trophic transitions between herbivory and carnivory occurring in sympatry with other established cichlid lineages. Tropheini evolved highly specialized eco-morphologies to exploit similar trophic niches in different ways repeatedly and rapidly. To better understand the evolutionary history and trophic adaptations of this lineage, we generated a dataset of 532 targeted loci from 21 out of the 22 described Tropheini species. We resolved the Tropheini into seven monophyletic genera and discovered one to be polyphyletic. The polyphyletic genus, Petrochromis, represents three convergent origins of the algae grazing trophic specialization. This repeated evolution of grazing may have been facilitated by adaptive introgression as we found evidence for gene flow among algae grazing genera. We also found evidence of gene flow among algae browsing genera, but gene flow was restricted between herbivorous and carnivorous genera. Furthermore, we observed no evidence supporting a hybrid origin of this radiation. Our molecular evolutionary analyses suggest that opsin genes likely evolved in response to selection pressures associated with trophic ecology in the Tropheini. We found surprisingly little evidence of positive selection in coding regions of jaw-shaping genes in this trophically diverse lineage. This suggests low degrees of freedom for further change in these genes, and possibly a larger role for regulatory variation in driving jaw adaptations. Our study emphasizes Tropheini cichlids as an important model for studying the evolution of trophic specialization and its role in speciation.
Collapse
Affiliation(s)
- Pooja Singh
- Institute of BiologyUniversity of GrazGrazAustria
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of BiologyUniversity of KonstanzConstanceGermany
- Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
| | - Iker Irisarri
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of BiologyUniversity of KonstanzConstanceGermany
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Museum HamburgHamburgGermany
| | - Julián Torres‐Dowdall
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of BiologyUniversity of KonstanzConstanceGermany
| | - Gerhard G. Thallinger
- Institute of Biomedical InformaticsGraz University of TechnologyGrazAustria
- OMICS Center Graz, BioTechMed GrazGrazAustria
| | - Hannes Svardal
- Department of BiologyUniversity of AntwerpAntwerpBelgium
- Naturalis Biodiversity CenterLeidenThe Netherlands
| | - Emily Moriarty Lemmon
- Department of Biological ScienceFlorida State University, Biomedical Research FacilityTallahasseeFloridaUSA
| | - Alan R. Lemmon
- Department of Biological ScienceFlorida State University, Biomedical Research FacilityTallahasseeFloridaUSA
| | | | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of BiologyUniversity of KonstanzConstanceGermany
| | | |
Collapse
|
15
|
Owen CL, Marshall DC, Wade EJ, Meister R, Goemans G, Kunte K, Moulds M, Hill K, Villet M, Pham TH, Kortyna M, Lemmon EM, Lemmon AR, Simon C. Detecting and removing sample contamination in phylogenomic data: an example and its implications for Cicadidae phylogeny (Insecta: Hemiptera). Syst Biol 2022; 71:1504-1523. [PMID: 35708660 DOI: 10.1093/sysbio/syac043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/23/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Contamination of a genetic sample with DNA from one or more non-target species is a continuing concern of molecular phylogenetic studies, both Sanger sequencing studies and Next-Generation Sequencing (NGS) studies. We developed an automated pipeline for identifying and excluding likely cross-contaminated loci based on detection of bimodal distributions of patristic distances across gene trees. When the contamination occurs between samples within a dataset, comparisons between a contaminated sample and its contaminant taxon will yield bimodal distributions with one peak close to zero patristic distance. This new method does not rely on a priori knowledge of taxon relatedness nor does it determine the causes(s) of the contamination. Exclusion of putatively contaminated loci from a dataset generated for the insect family Cicadidae showed that these sequences were affecting some topological patterns and branch supports, although the effects were sometimes subtle, with some contamination-influenced relationships exhibiting strong bootstrap support. Long tip branches and outlier values for one anchored phylogenomic pipeline statistic (AvgNHomologs) were correlated with the presence of contamination. While the AHE markers used here, which target hemipteroid taxa, proved effective in resolving deep and shallow level Cicadidae relationships in aggregate, individual markers contained inadequate phylogenetic signal, in part probably due to short length. The cleaned dataset, consisting of 429 loci, from 90 genera representing 44 of 56 current Cicadidae tribes, supported three of the four sampled Cicadidae subfamilies in concatenated-matrix maximum likelihood (ML) and multispecies coalescent-based species tree analyses, with the fourth subfamily weakly supported in the ML trees. No well-supported patterns from previous family-level Sanger sequencing studies of Cicadidae phylogeny were contradicted. One taxon (Aragualna plenalinea) did not fall with its current subfamily in the genetic tree, and this genus and its tribe Aragualnini is reclassified to Tibicininae following morphological re-examination. Only subtle differences were observed in trees after removal of loci for which divergent base frequencies were detected. Greater success may be achieved by increased taxon sampling and developing a probe set targeting a more recent common ancestor and longer loci. Searches for contamination are an essential step in phylogenomic analyses of all kinds and our pipeline is an effective solution.
Collapse
Affiliation(s)
- Christopher L Owen
- Systematic Entomology Laboratory, USDA-ARS, c/o National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - David C Marshall
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Elizabeth J Wade
- Dept. of Natural Science and Mathematics, Curry College, Milton, MA 02186, USA
| | - Russ Meister
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Geert Goemans
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Krushnamegh Kunte
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore 560 065, India
| | - Max Moulds
- Australian Museum Research Institute, 1 William Street, Sydney N.S.W, Australia. 2010
| | - Kathy Hill
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - M Villet
- Dept. of Biology, Rhodes University, Grahamstown 6140, South Africa
| | - Thai-Hong Pham
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, Hue, Vietnam.,Vietnam National Museum of Nature and Graduate School of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Michelle Kortyna
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University 400 Dirac Science Library, Tallahassee, FL 32306, USA
| | - Chris Simon
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| |
Collapse
|
16
|
Piller KR, Parker E, Lemmon AR, Moriarty Lemmon E. Investigating the utility of Anchored Hybrid Enrichment data to investigate the relationships among the Killifishes (Actinopterygii: Cyprinodontiformes), a globally distributed group of fishes. Mol Phylogenet Evol 2022; 173:107482. [PMID: 35452841 DOI: 10.1016/j.ympev.2022.107482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/06/2022] [Accepted: 04/06/2022] [Indexed: 10/18/2022]
Abstract
The Killifishes (Cyprinodontiformes) are a diverse and well-known group of fishes that contains sixteen families inclusive of Anablepidae, Aphaniidae Aplocheilidae, Cubanichthyidae, Cyprinodontidae, Fluviphylacidae, Fundulidae, Goodeidae, Nothobranchiidae, Orestiidae, Pantanodontidae, Poeciliidae, Procatopodidae, Profundulidae, Rivulidae, and Valenciidae and more than 1,200 species that are globally distributed in tropical and temperate, freshwater and estuarine habitats. The evolutionary relationships among the families within the group, based on different molecular and morphological data sets, have remained uncertain. Therefore, the objective of this study was to use a targeted approach, anchored hybrid enrichment, to investigate the phylogenetic relationships among the families within the Cyprindontiformes. This study included more than 100 individuals, representing all sixteen families within the Cyprinodontiformes, including many recently diagnosed families. We recovered an average of 244 loci per individual. These data were submitted to phylogenetic analyses (RaxML and ASTRAL) and although we recovered many of the same relationships as in previous studies of the group, several novel sets of relationships for other families also were recovered. In addition, two well-established clades (Suborders Cyprinodontoidei and Aplocheilodei) were recovered as monophyletic and are in agreement with most previous studies. We also assessed the degree of gene tree discordance in our dataset to evaluate support for alternative topological hypotheses for interfamilial relationships within the Cyprinodontiformes using a variety of different analyses. The results from this study will provide a robust, historical framework needed to investigate a plethora of biogeographic, taxonomic, ecological, and physiological questions for this group of fishes.
Collapse
Affiliation(s)
- Kyle R Piller
- Department of Biological Science, Southeastern Louisiana University, Hammond, LA 70402, USA.
| | - Elyse Parker
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, 32306-4120, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Biomedical Research Facility, Tallahassee, FL, 32306-4295, USA
| |
Collapse
|
17
|
Hernández-Gutiérrez R, van den Berg C, Granados Mendoza C, Peñafiel Cevallos M, Freire M. E, Lemmon EM, Lemmon AR, Magallón S. Localized Phylogenetic Discordance Among Nuclear Loci Due to Incomplete Lineage Sorting and Introgression in the Family of Cotton and Cacao (Malvaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:850521. [PMID: 35498660 PMCID: PMC9043901 DOI: 10.3389/fpls.2022.850521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
The economically important cotton and cacao family (Malvaceae sensu lato) have long been recognized as a monophyletic group. However, the relationships among some subfamilies are still unclear as discordant phylogenetic hypotheses keep arising when different sources of molecular data are analyzed. Phylogenetic discordance has previously been hypothesized to be the result of both introgression and incomplete lineage sorting (ILS), but the extent and source of discordance have not yet been evaluated in the context of loci derived from massive sequencing strategies and for a wide representation of the family. Furthermore, no formal methods have been applied to evaluate if the detected phylogenetic discordance among phylogenomic datasets influences phylogenetic dating estimates of the concordant relationships. The objective of this research was to generate a phylogenetic hypothesis of Malvaceae from nuclear genes, specifically we aimed to (1) investigate the presence of major discordance among hundreds of nuclear gene histories of Malvaceae; (2) evaluate the potential source of discordance; and (3) examine whether discordance and loci heterogeneity influence on time estimates of the origin and diversification of subfamilies. Our study is based on a comprehensive dataset representing 96 genera of the nine subfamilies and 268 nuclear loci. Both concatenated and coalescence-based approaches were followed for phylogenetic inference. Using branch lengths and topology, we located the placement of introgression events to directly evaluate whether discordance is due to introgression rather than ILS. To estimate divergence times, concordance and molecular rate were considered. We filtered loci based on congruence with the species tree and then obtained the molecular rate of each locus to distribute them into three different sets corresponding to shared molecular rate ranges. Bayesian dating was performed for each of the different sets of loci with the same parameters and calibrations. Phylogenomic discordance was detected between methods, as well as gene histories. At deep coalescent times, we found discordance in the position of five subclades probably due to ILS and a relatively small proportion of introgression. Divergence time estimation with each set of loci generated overlapping clade ages, indicating that, even with different molecular rate and gene histories, calibrations generally provide a strong prior.
Collapse
Affiliation(s)
- Rebeca Hernández-Gutiérrez
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Cássio van den Berg
- Departamento de Ciencias Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Carolina Granados Mendoza
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Efraín Freire M.
- Herbario Nacional del Ecuador (QCNE), Instituto Nacional de Biodiversidad, Quito, Ecuador
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, United States
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
18
|
Phylogeny and secondary sexual trait evolution in Schizocosa wolf spiders (Araneae, Lycosidae) shows evidence for multiple gains and losses of ornamentation and species delimitation uncertainty. Mol Phylogenet Evol 2022; 169:107397. [PMID: 35031456 DOI: 10.1016/j.ympev.2022.107397] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/27/2021] [Accepted: 12/27/2021] [Indexed: 12/18/2022]
Abstract
Members of the Nearctic spider genus Schizocosa Chamberlin, 1904 have garnered much attention in behavioral studies and over many decades, a number of species have developed as model systems for investigating patterns of sexual selection and multimodal communication. Many of these studies have employed a comparative approach using putative, but not rigorously tested, sister species pairs that have distinctive morphological traits and attendant behaviors. Despite past emphasis on the efficacy of these presumably comparative-based studies of closely related species, generating a robust phylogenetic hypothesis for Schizocosa has been an ongoing challenge. Here, we apply a phylogenomic approach using anchored hybrid enrichment to generate a data set comprising over 400 loci representing a comprehensive taxonomic sample of 23 Nearctic Schizocosa. Our sampling also includes numerous outgroup lycosid genera that allow for a robust evaluation of genus monophyly. Based on analyses using concatenation and coalescent-based methods, we recover a well-supported phylogeny that infers the following: 1) The New World Schizocosa do not form a monophyletic group; 2) Previous hypotheses of North American species require reconsideration along with the composition of species groups; 3) Multiple longstanding model species are not genealogically exclusive and thus are not "good" species; 4) This updated phylogenetic framework establishes a new working paradigm for studying the evolution of characters associated with reproductive communication and mating. Ancestral character state reconstructions show a complex pattern of homoplasy that has likely obfuscated previous attempts to reconstruct relationships and delimit species. Important characters presumably related to sexual selection, such as foreleg pigmentation and dense bristle formation, have undergone repeated gain and loss events, many of which have led to increased morphological divergence between sister-species. Evaluation of these traits in a comparative framework illuminates how sexual selection and natural selection influence character evolution and provides a model for future studies of multimodal communication evolution and function.
Collapse
|
19
|
OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
20
|
Douglas J, Jiménez-Silva CL, Bouckaert R. OUP accepted manuscript. Syst Biol 2022; 71:901-916. [PMID: 35176772 PMCID: PMC9248896 DOI: 10.1093/sysbio/syac010] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 11/16/2022] Open
Abstract
As genomic sequence data become increasingly available, inferring the phylogeny of the
species as that of concatenated genomic data can be enticing. However, this approach makes
for a biased estimator of branch lengths and substitution rates and an inconsistent
estimator of tree topology. Bayesian multispecies coalescent (MSC) methods address these
issues. This is achieved by constraining a set of gene trees within a species tree and
jointly inferring both under a Bayesian framework. However, this approach comes at the
cost of increased computational demand. Here, we introduce StarBeast3—a software package
for efficient Bayesian inference under the MSC model via Markov chain Monte Carlo. We gain
efficiency by introducing cutting-edge proposal kernels and adaptive operators, and
StarBeast3 is particularly efficient when a relaxed clock model is applied. Furthermore,
gene-tree inference is parallelized, allowing the software to scale with the size of the
problem. We validated our software and benchmarked its performance using three real and
two synthetic data sets. Our results indicate that StarBeast3 is up to one-and-a-half
orders of magnitude faster than StarBeast2, and therefore more than two orders faster than
*BEAST, depending on the data set and on the parameter, and can achieve convergence on
large data sets with hundreds of genes. StarBeast3 is open-source and is easy to set up
with a friendly graphical user interface. [Adaptive; Bayesian inference; BEAST 2;
effective population sizes; high performance; multispecies coalescent; parallelization;
phylogenetics.]
Collapse
Affiliation(s)
- Jordan Douglas
- School of Computer Science, University of Auckland, 9 Symonds
Street Level 1 Student Commons, Auckland 1010, New Zealand
- Correspondence to be sent to: School of Computer Science,
University of Auckland, 9 Symonds Street Level 1 Student Commons, Auckland 1010, New
Zealand; E-mail:
| | - Cinthy L Jiménez-Silva
- School of Computer Science, University of Auckland, 9 Symonds
Street Level 1 Student Commons, Auckland 1010, New Zealand
| | - Remco Bouckaert
- School of Computer Science, University of Auckland, 9 Symonds
Street Level 1 Student Commons, Auckland 1010, New Zealand
| |
Collapse
|
21
|
Montes de Oca L, Indicatti RP, Opatova V, Almeida M, Pérez-Miles F, Bond JE. Phylogenomic analysis, reclassification, and evolution of South American nemesioid burrowing mygalomorph spiders. Mol Phylogenet Evol 2021; 168:107377. [PMID: 34954378 DOI: 10.1016/j.ympev.2021.107377] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 11/30/2022]
Abstract
The family Nemesiidae was once among the most species-rich of mygalomorph spider families. However, over the past few decades both morphological and molecular studies focusing on mygalomorph phylogeny have recovered the group as paraphyletic. Hence, the systematics of the family Nemesiidae has more recently been controversial, with numerous changes at the family-group level and the recognition of the supra-familial clade Nemesioidina. Indeed, in a recent study by Opatova and collaborators, six nemesiid genera were transferred to the newly re-established family Pycnothelidae. Despite these changes, 12 South American nemesiid genera remained unplaced, and classified as incertae sedis due to shortcomings in taxon sampling. Accordingly, we evaluate the phylogenetic relationships of South American nemesioid species and genera with the principle aim of resolving their family level placement. Our work represents the most exhaustive phylogenomic sampling for South American Nemesiidae by including nine of the 12 genera described for the continent. Phylogenetic relationships were reconstructed using 457 loci obtained using the spider Anchored Hybrid Enrichment probe set. Based on these results Nemesiidae, Pycnothelidae, Microstigmatidae and Cyrtaucheniidae are not considered monophyletic. Our study also indicates that the lineage including the genus Fufius requires elevation to the family level (Rhytidicolidae Simon, 1903 (NEW RANK)). In Pycnothelidae, we recognize/delimit five subfamilies (Diplothelopsinae, Pionothelinae NEW SUBFAMILY, Prorachiinae NEW SUBFAMILY, Pselligminae NEW RANK, Pycnothelinae). We also transfer all the 12 South American nemesiid genera to Pycnothelidae: Chaco, Chilelopsis, Diplothelopsis, Flamencopsis, Hermachura, Longistylus, Lycinus, Neostothis, Prorachias, Psalistopoides, Pselligmus, Rachias. Additionally, we transferred the microstigmatid genus Xenonemesia to Pycnothelidae, and we propose the following generic synonymies and species transfers: Neostothis and Bayana are junior synonyms of Pycnothele (NEW SYNONYMY), as P. gigas and P. labordai, respectively (NEW COMBINATIONS); Hermachura is a junior synonym of Stenoterommata (NEW SYNONYMY), as S. luederwaldti (NEW COMBINATION); Flamencopsis is a junior synonym of Chilelopsis (NEW SYNONYMY), as C. minima (NEW COMBINATION); and Diplothelopsis is a junior synonym of Lycinus (NEW SYNONYMY), as L. ornatus and L. bonariensis (NEW COMBINATIONS). Considering the transferred genera and synonymies, Pycnothelidae now includes 15 described genera and 137 species. Finally, these results provide a robust phylogenetic framework that includes enhanced taxonomic sampling, for further resolving the biogeography and evolutionary time scale for the family Pycnothelidae.
Collapse
Affiliation(s)
- Laura Montes de Oca
- Sección Entomología, Facultad de Ciencias, Universidad de la República. Iguá 4225, 11400, Montevideo, Uruguay; Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura. Av. Italia 3318, 11600, Montevideo, Uruguay.
| | - Rafael P Indicatti
- Laboratório de Coleções Zoológicas, Instituto Butantan. Av. Vital Brazil, 1500 05503-900, São Paulo, São Paulo, Brazil; Departamento de Biodiversidade, Instituto de Biociências, Universidade Estadual Paulista, Av. 24A, 1515, CEP: 13.506-900, Rio Claro, São Paulo, Brazil.
| | - Vera Opatova
- Department of Zoology, Charles University, Faculty of Science, Viničná 7, 128 44 Prague, Czech Republic.
| | - Marlus Almeida
- Instituto Nacional de Pesquisas da Amazônia, Laboratório de Sistemática e Ecologia de Invertebrados do Solo, Av. André Araújo, 2936 - Petrópolis - Manaus, Amazonas, Brazil.
| | - Fernando Pérez-Miles
- Sección Entomología, Facultad de Ciencias, Universidad de la República. Iguá 4225, 11400, Montevideo, Uruguay
| | - Jason E Bond
- Department of Entomology and Nematology, University of California Davis, Academic Surge Building 1282, Davis, CA 95616, USA.
| |
Collapse
|
22
|
Miller CD, Forthman M, Miller CW, Kimball RT. Extracting ‘legacy loci’ from an invertebrate sequence capture data set. ZOOL SCR 2021. [DOI: 10.1111/zsc.12513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Caroline D. Miller
- Department of Entomology & Nematology University of Florida Gainesville FL USA
| | - Michael Forthman
- Department of Entomology & Nematology University of Florida Gainesville FL USA
- California State Collection of Arthropods Plant Pest Diagnostics Branch California Department of Food & Agriculture Sacramento CA USA
| | - Christine W. Miller
- Department of Entomology & Nematology University of Florida Gainesville FL USA
| | | |
Collapse
|
23
|
Duchêne DA, Mather N, Van Der Wal C, Ho SYW. Excluding loci with substitution saturation improves inferences from phylogenomic data. Syst Biol 2021; 71:676-689. [PMID: 34508605 PMCID: PMC9016599 DOI: 10.1093/sysbio/syab075] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 09/07/2021] [Indexed: 11/21/2022] Open
Abstract
The historical signal in nucleotide sequences becomes eroded over time by substitutions occurring repeatedly at the same sites. This phenomenon, known as substitution saturation, is recognized as one of the primary obstacles to deep-time phylogenetic inference using genome-scale data sets. We present a new test of substitution saturation and demonstrate its performance in simulated and empirical data. For some of the 36 empirical phylogenomic data sets that we examined, we detect substitution saturation in around 50% of loci. We found that saturation tends to be flagged as problematic in loci with highly discordant phylogenetic signals across sites. Within each data set, the loci with smaller numbers of informative sites are more likely to be flagged as containing problematic levels of saturation. The entropy saturation test proposed here is sensitive to high evolutionary rates relative to the evolutionary timeframe, while also being sensitive to several factors known to mislead phylogenetic inference, including short internal branches relative to external branches, short nucleotide sequences, and tree imbalance. Our study demonstrates that excluding loci with substitution saturation can be an effective means of mitigating the negative impact of multiple substitutions on phylogenetic inferences. [Phylogenetic model performance; phylogenomics; substitution model; substitution saturation; test statistics.]
Collapse
Affiliation(s)
- David A Duchêne
- Centre for Evolutionary Hologenomics, University of Copenhagen, 1352 Copenhagen, Denmark
| | - Niklas Mather
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Cara Van Der Wal
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| |
Collapse
|
24
|
Gene Flow and Diversification in Himalopsyche martynovi Species Complex (Trichoptera: Rhyacophilidae) in the Hengduan Mountains. BIOLOGY 2021; 10:biology10080816. [PMID: 34440048 PMCID: PMC8389565 DOI: 10.3390/biology10080816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022]
Abstract
The Hengduan Mountains are one of the most species-rich mountainous areas in the world. The origin and evolution of such a remarkable biodiversity are likely to be associated with geological or climatic dynamics, as well as taxon-specific biotic processes (e.g., hybridization, polyploidization, etc.). Here, we investigate the mechanisms fostering the diversification of the endemic Himalopsyche martynovi complex, a poorly known group of aquatic insects. We used multiple allelic datasets generated from 691 AHE loci to reconstruct species and RaxML phylogenetic trees. We selected the most reliable phylogenetic tree to perform network and gene flow analyses. The phylogenetic reconstructions and network analysis identified three clades, including H. epikur, H. martynovi sensu stricto and H. cf. martynovi. Himalopsyche martynovi sensu stricto and H. cf. martynovi present an intermediate morphology between H. epikur and H. viteceki, the closest known relative to the H. martynovi-complex. The gene flow analysis revealed extensive gene flow among these lineages. Our results suggest that H. viteceki and H. epikur are likely to have contributed to the evolution of H. martynovi sensu stricto and H. cf. martynovi via gene flow, and thus, our study provides insights in the diversification process of a lesser-known ecological group, and hints at the potential role of gene flow in the emergence of biological novelty in the Hengduan Mountains.
Collapse
|
25
|
Nicolas V, Mikula O, Lavrenchenko LA, Šumbera R, Bartáková V, Bryjová A, Meheretu Y, Verheyen E, Missoup AD, Lemmon AR, Moriarty Lemmon E, Bryja J. Phylogenomics of African radiation of Praomyini (Muridae: Murinae) rodents: First fully resolved phylogeny, evolutionary history and delimitation of extant genera. Mol Phylogenet Evol 2021; 163:107263. [PMID: 34273505 DOI: 10.1016/j.ympev.2021.107263] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 11/25/2022]
Abstract
The tribe Praomyini is a diversified group including 64 species and eight extant rodent genera. They live in a broad spectrum of habitats across whole sub-Saharan Africa. Members of this tribe are often very abundant, they have a key ecological role in ecosystems, they are hosts of many potentially pathogenic microorganisms and comprise numerous agricultural pests. Although this tribe is well supported by both molecular and morphological data, its intergeneric relationships and the species contents of several genera are not yet fully resolved. Recent molecular data suggest that at least three genera in current sense are paraphyletic. However, in these studies the species sampling was sparse and the resolution of relationships among genera was poor, probably due to a fast radiation of the tribe dated to the Miocene and insufficient amount of genetic data. Here we used genomic scale data (395 nuclear loci = 610,965 bp long alignment and mitogenomes = 14,745 bp) and produced the first fully resolved species tree containing most major lineages of the Praomyini tribe (i.e. all but one currently delimited genera and major intrageneric clades). Results of a fossil-based divergence dating analysis suggest that the radiation started during the Messinian stage (ca. 7 Ma) and was likely linked to a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forests, while many others adapted to a broad spectrum of new open lowland and montane habitats that appeared at the beginning of Pliocene. Our analyses clearly confirmed the presence of three polyphyletic genera (Praomys, Myomyscus and Mastomys). We review current knowledge of these three genera and suggest corresponding taxonomic changes. To keep genera monophyletic, we propose taxonomic re-arrangements and delimit four new genera. Furthermore, we discovered a new highly divergent genetic lineage of Praomyini in southwestern Ethiopia, which is described as a new species and genus.
Collapse
Affiliation(s)
- Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - Ondřej Mikula
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Leonid A Lavrenchenko
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii pr. 33, Moscow 119071, Russia
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Veronika Bartáková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Yonas Meheretu
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; Department of Biology and Institute of Mountain Research and Development, Mekelle University, Mekelle, Tigray, Ethiopia
| | - Erik Verheyen
- Royal Belgian Institute for Natural Sciences, Operational Direction Taxonomy and Phylogeny, 1000 Brussels, Belgium; Evolutionary Ecology Group, Biology Department, University of Antwerp, 2020 Antwerp, Belgium
| | - Alain Didier Missoup
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of Science, University of Douala, Douala, Cameroon
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4295, United States
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, United States
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic.
| |
Collapse
|
26
|
Vankan M, Ho SYW, Duchêne DA. Evolutionary Rate Variation Among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference. Syst Biol 2021; 71:490-500. [PMID: 34255084 PMCID: PMC8830059 DOI: 10.1093/sysbio/syab051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/18/2021] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic analyses of genomic data provide a powerful means of reconstructing the evolutionary relationships among organisms, yet such analyses are often hindered by conflicting phylogenetic signals among loci. Identifying the signals that are most influential to species-tree estimation can help to inform the choice of data for phylogenomic analysis. We investigated this in an analysis of 30 phylogenomic data sets. For each data set, we examined the association between several branch-length characteristics of gene trees and the distance between these gene trees and the corresponding species trees. We found that the distance of each gene tree to the species tree inferred from the full data set was positively associated with variation in root-to-tip distances and negatively associated with mean branch support. However, no such associations were found for gene-tree length, a measure of the overall substitution rate at each locus. We further explored the usefulness of the best-performing branch-based characteristics for selecting loci for phylogenomic analyses. We found that loci that yield gene trees with high variation in root-to-tip distances have a disproportionately distant signal of tree topology compared with the complete data sets. These results suggest that rate variation across lineages should be taken into consideration when exploring and even selecting loci for phylogenomic analysis.[Branch support; data filtering; nucleotide substitution model; phylogenomics; substitution rate; summary coalescent methods.]
Collapse
Affiliation(s)
- Mezzalina Vankan
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia.,Research School of Biology, Australian National University, ACT 2601, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - David A Duchêne
- Research School of Biology, Australian National University, ACT 2601, Australia.,Centre for Evolutionary Hologenomics, University of Copenhagen, Copenhagen 1352, Denmark
| |
Collapse
|
27
|
Gene flow in phylogenomics: Sequence capture resolves species limits and biogeography of Afromontane forest endemic frogs from the Cameroon Highlands. Mol Phylogenet Evol 2021; 163:107258. [PMID: 34252546 DOI: 10.1016/j.ympev.2021.107258] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 06/28/2021] [Accepted: 07/07/2021] [Indexed: 11/21/2022]
Abstract
Puddle frogs of the Phrynobatrachus steindachneri species complex are a useful group for investigating speciation and phylogeography in Afromontane forests of the Cameroon Volcanic Line, western Central Africa. The species complex is represented by six morphologically relatively cryptic mitochondrial DNA lineages, only two of which are distinguished at the species level - southern P. jimzimkusi and Lake Oku endemic P. njiomock, leaving the remaining four lineages identified as 'P. steindachneri'. In this study, the six mtDNA lineages are subjected to genomic sequence capture analyses and morphological examination to delimit species and to study biogeography. The nuclear DNA data (387 loci; 571,936 aligned base pairs) distinguished all six mtDNA lineages, but the topological pattern and divergence depths supported only four main clades: P. jimzimkusi, P. njiomock, and only two divergent evolutionary lineages within the four 'P. steindachneri' mtDNA lineages. One of the two lineages is herein described as a new species, P. amieti sp. nov. Reticulate evolution (hybridization) was detected within the species complex with morphologically intermediate hybrid individuals placed between the parental species in phylogenomic analyses, forming a ladder-like phylogenetic pattern. The presence of hybrids is undesirable in standard phylogenetic analyses but is essential and beneficial in the network multispecies coalescent. This latter approach provided insight into the reticulate evolutionary history of these endemic frogs. Introgressions likely occurred during the Middle and Late Pleistocene climatic oscillations, due to the cyclic connections (likely dominating during cold glacials) and separations (during warm interglacials) of montane forests. The genomic phylogeographic pattern supports the separation of the southern (Mt. Manengouba to Mt. Oku) and northern mountains at the onset of the Pleistocene. Further subdivisions occurred in the Early Pleistocene, separating populations from the northernmost (Tchabal Mbabo, Gotel Mts.) and middle mountains (Mt. Mbam, Mt. Oku, Mambilla Plateau), as well as the microendemic lineage restricted to Lake Oku (Mt. Oku). This unique model system is highly threatened as all the species within the complex have exhibited severe population declines in the past decade, placing them on the brink of extinction. In addition, Mount Oku is identified to be of particular conservation importance because it harbors three species of this complex. We, therefore, urge for conservation actions in the Cameroon Highlands to preserve their diversity before it is too late.
Collapse
|
28
|
Douglas HB, Kundrata R, Brunke AJ, Escalona HE, Chapados JT, Eyres J, Richter R, Savard K, Ślipiński A, McKenna D, Dettman JR. Anchored Phylogenomics, Evolution and Systematics of Elateridae: Are All Bioluminescent Elateroidea Derived Click Beetles? BIOLOGY 2021; 10:biology10060451. [PMID: 34063961 PMCID: PMC8224040 DOI: 10.3390/biology10060451] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/21/2022]
Abstract
Simple Summary In the era of phylogenomics, new molecular sequencing and computational techniques can aid in resolving phylogenetic relationships that were previously intractable by morphological or limited molecular data. In this study, we used anchored hybrid enrichment—designed to recover DNA sequences from hundreds of single-copy orthologous genes—to resolve the phylogeny of the Elateridae (click-beetles) and establish their placement within superfamily Elateroidea. The resulting data were compatible with published transcriptomes, allowing for integrating our dataset with previously published data. Using a wide range of analyses on these molecular data, we tested hypotheses long-debated in the morphological literature and also the robustness of our phylogenetic inferences. Our results placed the bioluminescent lampyroids (fireflies and relatives) within the click-beetles, challenging the current classification of Elateridae, Lampyridae, Phengodidae, and Rhagophthalmidae. However, despite the large amount of molecular data analyzed, a few nodes with conflicting phylogenetic signals could not be unambiguously resolved. Overall, we recovered well-resolved tree topologies that will serve as a framework for further systematic and evolutionary studies of click-beetles. This work further demonstrates that the click-beetle lineage contains not only pest wireworms, but also many species that benefit agriculture. Abstract Click-beetles (Coleoptera: Elateridae) are an abundant, diverse, and economically important beetle family that includes bioluminescent species. To date, molecular phylogenies have sampled relatively few taxa and genes, incompletely resolving subfamily level relationships. We present a novel probe set for anchored hybrid enrichment of 2260 single-copy orthologous genes in Elateroidea. Using these probes, we undertook the largest phylogenomic study of Elateroidea to date (99 Elateroidea, including 86 Elateridae, plus 5 non-elateroid outgroups). We sequenced specimens from 88 taxa to test the monophyly of families, subfamilies and tribes. Maximum likelihood and coalescent phylogenetic analyses produced well-resolved topologies. Notably, the included non-elaterid bioluminescent families (Lampyridae + Phengodidae + Rhagophthalmidae) form a clade within the otherwise monophyletic Elateridae, and Sinopyrophoridae may not warrant recognition as a family. All analyses recovered the elaterid subfamilies Elaterinae, Agrypninae, Cardiophorinae, Negastriinae, Pityobiinae, and Tetralobinae as monophyletic. Our results were conflicting on whether the hypnoidines are sister to Dendrometrinae or Cardiophorinae + Negastriinae. Moreover, we show that fossils with the eucnemid-type frons and elongate cylindrical shape may belong to Eucnemidae, Elateridae: Thylacosterninae, ancestral hard-bodied cantharoids or related extinct groups. Proposed taxonomic changes include recognition of Plastocerini as a tribe in Dendrometrinae and Hypnoidinae stat. nov. as a subfamily within Elateridae.
Collapse
Affiliation(s)
- Hume B. Douglas
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada; (A.J.B.); (J.T.C.); (J.E.); (R.R.); (K.S.); (J.R.D.)
- Correspondence:
| | - Robin Kundrata
- Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic;
| | - Adam J. Brunke
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada; (A.J.B.); (J.T.C.); (J.E.); (R.R.); (K.S.); (J.R.D.)
| | - Hermes E. Escalona
- Australian National Insect Collection, National Collections Australia, CSIRO, Canberra, ACT 2601, Australia; (H.E.E.); (A.Ś.)
| | - Julie T. Chapados
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada; (A.J.B.); (J.T.C.); (J.E.); (R.R.); (K.S.); (J.R.D.)
| | - Jackson Eyres
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada; (A.J.B.); (J.T.C.); (J.E.); (R.R.); (K.S.); (J.R.D.)
| | - Robin Richter
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada; (A.J.B.); (J.T.C.); (J.E.); (R.R.); (K.S.); (J.R.D.)
| | - Karine Savard
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada; (A.J.B.); (J.T.C.); (J.E.); (R.R.); (K.S.); (J.R.D.)
| | - Adam Ślipiński
- Australian National Insect Collection, National Collections Australia, CSIRO, Canberra, ACT 2601, Australia; (H.E.E.); (A.Ś.)
| | - Duane McKenna
- Center for Biodiversity Research, Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA;
| | - Jeremy R. Dettman
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada; (A.J.B.); (J.T.C.); (J.E.); (R.R.); (K.S.); (J.R.D.)
| |
Collapse
|
29
|
Nguyen HDT, McCormick W, Eyres J, Eggertson Q, Hambleton S, Dettman JR. Development and evaluation of a target enrichment bait set for phylogenetic analysis of oomycetes. Mycologia 2021; 113:856-867. [PMID: 33945437 DOI: 10.1080/00275514.2021.1889276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Target enrichment is a term that encompasses multiple related approaches where desired genomic regions are captured by molecular baits, leaving behind redundant or non-target regions in the genome, followed by amplification and next-generation sequencing of those captured regions. A molecular bait set was developed based on 426 single-copy, oomycete-specific orthologs and 3 barcoding genes. The bait set was tested on 27 oomycete samples (belonging to the Saprolegniales, Albuginales, and Peronosporales) derived from live and herbarium specimens, as well as control samples of true fungi and plants. Results show that (i) our method greatly enriches for the targeted orthologs on oomycete samples, but insignificantly on fungal and plant samples; (ii) an average of 263 out of 429 orthologs (61%) were recovered from oomycete live and herbarium specimens; (iii) sequencing roughly 100 000 read pairs per sample is sufficient for optimal ortholog recovery while maintaining low sequencing costs; and (iv) the expected relationships were recovered by phylogenetic analysis from the data generated. This is the first report of an oomycete-specific target enrichment method with broad potential applications for evolutionary and taxonomic studies. A key benefit of our target enrichment method is that it allows researchers to easily unlock the vast and unexplored oomycete genomic diversity stored in natural history collections.
Collapse
Affiliation(s)
- Hai D T Nguyen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
| | - Wayne McCormick
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
| | - Jackson Eyres
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
| | - Quinn Eggertson
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
| | - Sarah Hambleton
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
| | - Jeremy R Dettman
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
| |
Collapse
|
30
|
Nydam ML, Lemmon AR, Cherry JR, Kortyna ML, Clancy DL, Hernandez C, Cohen CS. Phylogenomic and morphological relationships among the botryllid ascidians (Subphylum Tunicata, Class Ascidiacea, Family Styelidae). Sci Rep 2021; 11:8351. [PMID: 33863944 PMCID: PMC8052435 DOI: 10.1038/s41598-021-87255-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/16/2021] [Indexed: 02/02/2023] Open
Abstract
Ascidians (Phylum Chordata, Class Ascidiacea) are a large group of invertebrates which occupy a central role in the ecology of marine benthic communities. Many ascidian species have become successfully introduced around the world via anthropogenic vectors. The botryllid ascidians (Order Stolidobranchia, Family Styelidae) are a group of 53 colonial species, several of which are widespread throughout temperate or tropical and subtropical waters. However, the systematics and biology of this group of ascidians is not well-understood. To provide a systematic framework for this group, we have constructed a well-resolved phylogenomic tree using 200 novel loci and 55 specimens. A Principal Components Analysis of all species described in the literature using 31 taxonomic characteristics revealed that some species occupy a unique morphological space and can be easily identified using characteristics of adult colonies. For other species, additional information such as larval or life history characteristics may be required for taxonomic discrimination. Molecular barcodes are critical for guiding the delineation of morphologically similar species in this group.
Collapse
Affiliation(s)
- Marie L Nydam
- Math and Science Program, Soka University of America, 1 University Drive, Aliso Viejo, CA, 92656, USA.
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, 400 Dirac Science Library, Tallahassee, FL, 32306, USA
| | - Jesse R Cherry
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL, 32306, USA
| | - Michelle L Kortyna
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL, 32306, USA
| | - Darragh L Clancy
- Biology Department and Estuarine and Ocean Science Center, San Francisco State University, 3150 Paradise Drive, Tiburon, CA, 94920, USA
| | - Cecilia Hernandez
- Biology Department and Estuarine and Ocean Science Center, San Francisco State University, 3150 Paradise Drive, Tiburon, CA, 94920, USA
| | - C Sarah Cohen
- Biology Department and Estuarine and Ocean Science Center, San Francisco State University, 3150 Paradise Drive, Tiburon, CA, 94920, USA
| |
Collapse
|
31
|
Warwick AR, Barrow LN, Smith ML, Means DB, Lemmon AR, Lemmon EM. Signatures of north-eastern expansion and multiple refugia: genomic phylogeography of the Pine Barrens tree frog, Hyla andersonii (Anura: Hylidae). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Range fragmentation poses challenges for species persistence over time and can be caused by both historical and contemporary processes. We combined genomic data, phylogeographical model testing and palaeoclimatic niche modelling to infer the evolutionary history of the Pine Barrens tree frog (Hyla andersonii), a seepage bog specialist, in eastern North America to gain a better understanding of the historical context of its fragmented distribution. We sampled H. andersonii populations across the three disjunct regions of the species range: Alabama/Florida (AF), the Carolinas (CL) and New Jersey (NJ). Phylogenetic relationships within H. andersonii were consistent between the nuclear species tree and mitochondrial analyses, indicating divergence between AF and CL/NJ (Atlantic clade) ~0.9 Mya and divergence of the NJ clade ~0.15 Mya. Several predictions of north-eastern expansion along the Atlantic coast were supported by phylogeographical analyses. Model testing using genome-wide single nucleotide polymorphism data and species distribution models both provided evidence for multiple disjunct refugia. This comprehensive phylogeographical study of H. andersonii demonstrates a long history of range fragmentation within an endemic coastal plain species and highlights the influence of historical climate change on the current distribution of species and their genetic diversity.
Collapse
Affiliation(s)
- Alexa R Warwick
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Lisa N Barrow
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Megan L Smith
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN, USA
| | - D Bruce Means
- Coastal Plains Institute and Land Conservancy, Tallahassee, FL, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, USA
| | | |
Collapse
|
32
|
Rix MG, Wilson JD, Huey JA, Hillyer MJ, Gruber K, Harvey MS. Diversification of the mygalomorph spider genus Aname (Araneae: Anamidae) across the Australian arid zone: Tracing the evolution and biogeography of a continent-wide radiation. Mol Phylogenet Evol 2021; 160:107127. [PMID: 33667632 DOI: 10.1016/j.ympev.2021.107127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/26/2021] [Accepted: 02/24/2021] [Indexed: 02/08/2023]
Abstract
The assembly of the Australian arid zone biota has long fascinated biogeographers. Covering over two-thirds of the continent, Australia's vast arid zone biome is home to a distinctive fauna and flora, including numerous lineages which have diversified since the Eocene. Tracing the origins and speciation history of these arid zone taxa has been an ongoing endeavour since the advent of molecular phylogenetics, and an increasing number of studies on invertebrate animals are beginning to complement a rich history of research on vertebrate and plant taxa. In this study, we apply continent-wide genetic sampling and one of the largest phylogenetic data matrices yet assembled for a genus of Australian spiders, to reconstruct the phylogeny and biogeographic history of the open-holed trapdoor spider genus Aname L. Koch, 1873. This highly diverse lineage of Australian mygalomorph spiders has a distribution covering the majority of Australia west of the Great Dividing Range, but apparently excluding the high rainfall zones of eastern Australia and Tasmania. Original and legacy sequences were obtained for three mtDNA and four nuDNA markers from 174 taxa in seven genera, including 150 Aname specimen terminals belonging to 102 species-level operational taxonomic units, sampled from 32 bioregions across Australia. Reconstruction of the phylogeny and biogeographic history of Aname revealed three radiations (Tropical, Temperate-Eastern and Continental), which could be further broken into eight major inclusive clades. Ancestral area reconstruction revealed the Pilbara, Monsoon Tropics and Mid-West to be important ancestral areas for the genus Aname and its closest relatives, with the origin of Aname itself inferred in the Pilbara bioregion. From these origins in the arid north-west of Australia, our study found evidence for a series of subsequent biome transitions in separate lineages, with at least eight tertiary incursions back into the arid zone from more mesic tropical, temperate or eastern biomes, and only two major clades which experienced widespread (primary) in situ diversification within the arid zone. Based on our phylogenetic results, and results from independent legacy divergence dating studies, we further reveal the importance of climate-driven biotic change in the Miocene and Pliocene in shaping the distribution and composition of the Australian arid zone biota, and the value of continent-wide studies in revealing potentially complex patterns of arid zone diversification in dispersal-limited invertebrate taxa.
Collapse
Affiliation(s)
- Michael G Rix
- Biodiversity and Geosciences Program, Queensland Museum, South Brisbane, QLD 4101, Australia; Collections and Research Centre, Western Australian Museum, Welshpool, WA 6106, Australia.
| | - Jeremy D Wilson
- Biodiversity and Geosciences Program, Queensland Museum, South Brisbane, QLD 4101, Australia; Division of Arachnology, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Av. Ángel Gallardo 470 (C1405DJR), Buenos Aires, Argentina
| | - Joel A Huey
- Collections and Research Centre, Western Australian Museum, Welshpool, WA 6106, Australia; School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Mia J Hillyer
- Collections and Research Centre, Western Australian Museum, Welshpool, WA 6106, Australia
| | - Karl Gruber
- Collections and Research Centre, Western Australian Museum, Welshpool, WA 6106, Australia; School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Mark S Harvey
- Collections and Research Centre, Western Australian Museum, Welshpool, WA 6106, Australia; School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| |
Collapse
|
33
|
Percequillo AR, Prado JRD, Abreu EF, Dalapicolla J, Pavan AC, de Almeida Chiquito E, Brennand P, Steppan SJ, Lemmon AR, Lemmon EM, Wilkinson M. Tempo and mode of evolution of oryzomyine rodents (Rodentia, Cricetidae, Sigmodontinae): A phylogenomic approach. Mol Phylogenet Evol 2021; 159:107120. [PMID: 33610650 DOI: 10.1016/j.ympev.2021.107120] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 02/01/2021] [Accepted: 02/09/2021] [Indexed: 11/19/2022]
Abstract
The tribe Oryzomyini is an impressive group of rodents, comprising 30 extant genera and an estimated 147 species. Recent remarkable advances in the understanding of the diversity, taxonomy and systematics of the tribe have mostly derived from analyses of single or few genetic markers. However, the evolutionary history and biogeography of Oryzomyini, its origin and diversification across the Neotropics, remain unrevealed. Here we use a multi-locus dataset (over 400 loci) obtained through anchored phylogenomics to provide a genome-wide phylogenetic hypothesis for Oryzomyini and to investigate the tempo and mode of its evolution. Species tree and supermatrix analyses produced topologies with strong support for most branches, with all genera confirmed as monophyletic, a result that previous studies failed to obtain. Our analyses also corroborated the monophyly and phylogenetic relationship of three main clades of Oryzomyini (B, C and D). The origin of the tribe is estimated to be in the Miocene (8.93-5.38 million years ago). The cladogenetic events leading to the four main clades occurred during the late Miocene and early Pliocene and most speciation events in the Pleistocene. Geographic range estimates suggested an east of Andes origin for the ancestor of oryzomyines, most likely in the Boreal Brazilian region, which includes the north bank of Rio Amazonas and the Guiana Shield. Oryzomyini rodents are an autochthonous South America radiation, that colonized areas and dominions of this continent mainly by dispersal events. The evolutionary history of the tribe is deeply associated with the Andean cordillera and the landscape history of Amazon basin.
Collapse
Affiliation(s)
- Alexandre Reis Percequillo
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900 Piracicaba, São Paulo, Brazil; Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK.
| | - Joyce Rodrigues do Prado
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900 Piracicaba, São Paulo, Brazil.
| | - Edson Fiedler Abreu
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900 Piracicaba, São Paulo, Brazil.
| | - Jeronymo Dalapicolla
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900 Piracicaba, São Paulo, Brazil; Instituto Tecnológico Vale, Desenvolvimento Sustentável, 66055-090 Belém, PA, Brazil.
| | - Ana Carolina Pavan
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900 Piracicaba, São Paulo, Brazil.
| | - Elisandra de Almeida Chiquito
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900 Piracicaba, São Paulo, Brazil; Laboratório de Mastozoologia e Biogeografia, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, 29075-910 Vitória, ES, Brazil.
| | - Pamella Brennand
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900 Piracicaba, São Paulo, Brazil.
| | - Scott J Steppan
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA.
| | - Alan R Lemmon
- Department of Scientific Computing, 400 Dirac Science Library, Florida State University, Tallahassee, FL 32306, USA.
| | - Emily Moriarty Lemmon
- Department of Scientific Computing, 400 Dirac Science Library, Florida State University, Tallahassee, FL 32306, USA.
| | - Mark Wilkinson
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK.
| |
Collapse
|
34
|
Bybee SM, Kalkman VJ, Erickson RJ, Frandsen PB, Breinholt JW, Suvorov A, Dijkstra KDB, Cordero-Rivera A, Skevington JH, Abbott JC, Sanchez Herrera M, Lemmon AR, Moriarty Lemmon E, Ware JL. Phylogeny and classification of Odonata using targeted genomics. Mol Phylogenet Evol 2021; 160:107115. [PMID: 33609713 DOI: 10.1016/j.ympev.2021.107115] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 01/25/2021] [Accepted: 02/08/2021] [Indexed: 11/29/2022]
Abstract
Dragonflies and damselflies are a charismatic, medium-sized insect order (~6300 species) with a unique potential to approach comparative research questions. Their taxonomy and many ecological traits for a large fraction of extant species are relatively well understood. However, until now, the lack of a large-scale phylogeny based on high throughput data with the potential to connect both perspectives has precluded comparative evolutionary questions for these insects. Here, we provide an ordinal hypothesis of classification based on anchored hybrid enrichment using a total of 136 species representing 46 of the 48 families or incertae sedis, and a total of 478 target loci. Our analyses recovered the monophyly for all three suborders: Anisoptera, Anisozygoptera and Zygoptera. Although the backbone of the topology was reinforced and showed the highest support values to date, our genomic data was unable to stronglyresolve portions of the topology. In addition, a quartet sampling approach highlights the potential evolutionary scenarios that may have shaped evolutionary phylogeny (e.g., incomplete lineage sorting and introgression) of this taxon. Finally, in light of our phylogenomic reconstruction and previous morphological and molecular information we proposed an updated odonate classification and define five new families (Amanipodagrionidae fam. nov., Mesagrionidae fam. nov., Mesopodagrionidae fam. nov., Priscagrionidae fam. nov., Protolestidae fam. nov.) and reinstate another two (Rhipidolestidae stat. res., Tatocnemididae stat. res.). Additionally, we feature the problematic taxonomic groupings for examination in future studies to improve our current phylogenetic hypothesis.
Collapse
Affiliation(s)
- Seth M Bybee
- Department of Biology and Monte L. Bean Museum, Brigham Young University, USA.
| | | | - Robert J Erickson
- Department of Biology and Monte L. Bean Museum, Brigham Young University, USA
| | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, USA; Data Science Lab, Smithsonian Institution, USA
| | - Jesse W Breinholt
- Intermountain Healthcare, Intermountain Precision Genomics, USA; RAPiD Genomics, USA; McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, USA
| | - Anton Suvorov
- Department of Genetics, University of North Carolina at Chapel Hill, USA
| | | | | | - Jeffrey H Skevington
- Agriculture and Agri-Food Canada, Canadian National Collection of Insects, Canada
| | - John C Abbott
- Alabama Museum of Natural History, Department of Research and Collections, The University of Alabama, USA
| | | | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, USA
| | | | - Jessica L Ware
- Division of Invertebrate Zoology, American Museum of Natural History, USA
| |
Collapse
|
35
|
Hurt C, Hultgren K, Anker A, Lemmon AR, Moriarty Lemmon E, Bracken-Grissom H. First worldwide molecular phylogeny of the morphologically and ecologically hyperdiversified snapping shrimp genus Alpheus (Malacostraca: Decapoda). Mol Phylogenet Evol 2021; 158:107080. [PMID: 33482381 DOI: 10.1016/j.ympev.2021.107080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 11/26/2022]
Abstract
Hyperdiverse animal groups raise intriguing questions regarding the factors that generate and maintain their diversity. The snapping shrimp genus Alpheus (with >300 described species) is a spectacularly diversified group of decapod crustaceans that serves as an exemplary system for addressing evolutionary questions regarding morphological adaptations, symbiosis, cryptic diversity and molecular divergence. A lack of information regarding evolutionary relationships among species has limited investigations into the mechanisms that drive the diversification of Alpheus. Previous phylogenetic studies of Alpheus have been restricted in scope, while molecular datasets used for phylogenetic reconstructions have been based solely on mitochondrial and a handful of nuclear markers. Here we use an anchored hybrid enrichment (AHE) approach to resolve phylogenetic relationships among species of Alpheus. The AHE method generated sequence data for 240 loci (>72,000 bp) for 65 terminal species that span the geographic, ecological and taxonomic diversity of Alpheus. Our resulting, well-supported phylogeny demonstrates a lack of monophyly for five out of seven morphologically defined species groups that have traditionally been used as a framework in Alpheus taxonomy. Our results also suggest that symbiotic associations with a variety of other animals have evolved independently in at least seven lineages in this genus. Our AHE phylogeny represents the most comprehensive phylogenetic treatment of Alpheus to date and will provide a useful evolutionary framework to further investigate questions, such as various modifications of the snapping claw and the role of habitat specialization and symbiosis in promoting speciation. Running head: PHYLOGENY OF THE SNAPPING SHRIMP GENUS ALPHEUS.
Collapse
Affiliation(s)
- Carla Hurt
- Department of Biology, Tennessee Tech University, Cookeville, TN 38505, United States.
| | - Kristin Hultgren
- Department of Biology, Seattle University, Seattle, WA 98122, United States.
| | - Arthur Anker
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiás, Brazil
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306-4120, United States; Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, United States
| | - Emily Moriarty Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306-4120, United States; Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, United States
| | - Heather Bracken-Grissom
- Institute of Environment and Department of Biological Sciences, Florida International University-Biscayne Bay Campus, North Miami, FL 33181, United States
| |
Collapse
|
36
|
Mikula O, Nicolas V, Šumbera R, Konečný A, Denys C, Verheyen E, Bryjová A, Lemmon AR, Moriarty Lemmon E, Bryja J. Nuclear phylogenomics, but not mitogenomics, resolves the most successful Late Miocene radiation of African mammals (Rodentia: Muridae: Arvicanthini). Mol Phylogenet Evol 2021; 157:107069. [PMID: 33421615 DOI: 10.1016/j.ympev.2021.107069] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 12/17/2020] [Accepted: 01/04/2021] [Indexed: 01/09/2023]
Abstract
The tribe Arvicanthini (Muridae: Murinae) is a highly diversified group of rodents (ca. 100 species) and with 18 African genera (plus one Asiatic) represents probably the most successful adaptive radiation of extant mammals in Africa. They colonized a broad spectrum of habitats (from rainforests to semi-deserts) in whole sub-Saharan Africa and their members often belong to most abundant parts of mammal communities. Despite intensive efforts, the phylogenetic relationships among major lineages (i.e. genera) remained obscured, which was likely caused by the intensive radiation of the group, dated to the Late Miocene. Here we used genomic scale data (377 nuclear loci; 581,030 bp) and produced the first fully resolved species tree containing all currently delimited genera of the tribe. Mitogenomes were also extracted, and while the results were largely congruent, there was less resolution at basal nodes of the mitochondrial phylogeny. Results of a fossil-based divergence dating analysis suggest that the African radiation started early after the colonization of Africa by a single arvicanthine ancestor from Asia during the Messinian stage (ca. 7 Ma), and was likely linked with a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forest, while many others successfully colonized broad spectrum of new open habitats (e.g. savannas, wetlands or montane moorlands) that appeared at the beginning of Pliocene. One lineage even evolved partially arboricolous life style in savanna woodlands, which allowed them to re-colonize equatorial forests. We also discuss delimitation of genera in Arvicanthini and propose corresponding taxonomic changes.
Collapse
Affiliation(s)
- Ondřej Mikula
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, 602 00 Brno, Czech Republic
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Adam Konečný
- Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - Erik Verheyen
- Royal Belgian Institute for Natural Sciences, Operational Direction Taxonomy and Phylogeny, 1000 Brussels, Belgium; Evolutionary Ecology Group, Biology Department, University of Antwerp, 2020 Antwerp, Belgium
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4295, United States
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, United States
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic.
| |
Collapse
|
37
|
Banker SE, Lemmon AR, Hassinger AB, Dye M, Holland SD, Kortyna ML, Ospina OE, Ralicki H, Lemmon EM. Hierarchical Hybrid Enrichment: Multitiered Genomic Data Collection Across Evolutionary Scales, With Application to Chorus Frogs (Pseudacris). Syst Biol 2021; 69:756-773. [PMID: 31886503 PMCID: PMC7302053 DOI: 10.1093/sysbio/syz074] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 10/26/2019] [Accepted: 11/04/2019] [Indexed: 01/25/2023] Open
Abstract
Determining the optimal targets of genomic subsampling for phylogenomics, phylogeography, and population genomics remains a challenge for evolutionary biologists. Of the available methods for subsampling the genome, hybrid enrichment (sequence capture) has become one of the primary means of data collection for systematics, due to the flexibility and cost efficiency of this approach. Despite the utility of this method, information is lacking as to what genomic targets are most appropriate for addressing questions at different evolutionary scales. In this study, first, we compare the benefits of target loci developed for deep- and shallow scales by comparing these loci at each of three taxonomic levels: within a genus (phylogenetics), within a species (phylogeography), and within a hybrid zone (population genomics). Specifically, we target evolutionarily conserved loci that are appropriate for deeper phylogenetic scales and more rapidly evolving loci that are informative for phylogeographic and population genomic scales. Second, we assess the efficacy of targeting multiple-locus sets for different taxonomic levels in the same hybrid enrichment reaction, an approach we term hierarchical hybrid enrichment. Third, we apply this approach to the North American chorus frog genus Pseudacris to answer key evolutionary questions across taxonomic and temporal scales. We demonstrate that in this system the type of genomic target that produces the most resolved gene trees differs depending on the taxonomic level, although the potential for error is substantially lower for the deep-scale loci at all levels. We successfully recover data for the two different locus sets with high efficiency. Using hierarchical data targeting deep and shallow levels: we 1) resolve the phylogeny of the genus Pseudacris and introduce a novel visual and hypothesis testing method that uses nodal heat maps to examine the robustness of branch support values to the removal of sites and loci; 2) estimate the phylogeographic history of Pseudacris feriarum, which reveals up to five independent invasions leading to sympatry with congener Pseudacris nigrita to form replicated reinforcement contact zones with ongoing gene flow into sympatry; and 3) quantify with high confidence the frequency of hybridization in one of these zones between P. feriarum and P. nigrita, which is lower than microsatellite-based estimates. We find that the hierarchical hybrid enrichment approach offers an efficient, multitiered data collection method for simultaneously addressing questions spanning multiple evolutionary scales. [Anchored hybrid enrichment; heat map; hybridization; phylogenetics; phylogeography; population genomics; reinforcement; reproductive character displacement.].
Collapse
Affiliation(s)
- Sarah E Banker
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.,Department of Integrative Biology, University of California, Berkeley, #3160 Berkeley, CA 94720-3160, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University 400 Dirac Science Library, Tallahassee, FL 32306, USA
| | - Alyssa Bigelow Hassinger
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.,Department of Evolution, Ecology, and Organismal Biology, Ohio State University, 318 W. 12th Avenue, 300 Aronoff Laboratory, Columbus, OH 43210, USA
| | - Mysia Dye
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Sean D Holland
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Michelle L Kortyna
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Oscar E Ospina
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Hannah Ralicki
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.,Department of Biological Science, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06268, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| |
Collapse
|
38
|
Opatova V, Hamilton CA, Hedin M, De Oca LM, Král J, Bond JE. Phylogenetic Systematics and Evolution of the Spider Infraorder Mygalomorphae Using Genomic Scale Data. Syst Biol 2021; 69:671-707. [PMID: 31841157 DOI: 10.1093/sysbio/syz064] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 09/10/2019] [Indexed: 12/19/2022] Open
Abstract
The infraorder Mygalomorphae is one of the three main lineages of spiders comprising over 3000 nominal species. This ancient group has a worldwide distribution that includes among its ranks large and charismatic taxa such as tarantulas, trapdoor spiders, and highly venomous funnel-web spiders. Based on past molecular studies using Sanger-sequencing approaches, numerous mygalomorph families (e.g., Hexathelidae, Ctenizidae, Cyrtaucheniidae, Dipluridae, and Nemesiidae) have been identified as non-monophyletic. However, these data were unable to sufficiently resolve the higher-level (intra- and interfamilial) relationships such that the necessary changes in classification could be made with confidence. Here, we present a comprehensive phylogenomic treatment of the spider infraorder Mygalomorphae. We employ 472 loci obtained through anchored hybrid enrichment to reconstruct relationships among all the mygalomorph spider families and estimate the timeframe of their diversification. We sampled nearly all currently recognized families, which has allowed us to assess their status, and as a result, propose a new classification scheme. Our generic-level sampling has also provided an evolutionary framework for revisiting questions regarding silk use in mygalomorph spiders. The first such analysis for the group within a strict phylogenetic framework shows that a sheet web is likely the plesiomorphic condition for mygalomorphs, as well as providing insights to the ancestral foraging behavior for all spiders. Our divergence time estimates, concomitant with detailed biogeographic analysis, suggest that both ancient continental-level vicariance and more recent dispersal events have played an important role in shaping modern day distributional patterns. Based on our results, we relimit the generic composition of the Ctenizidae, Cyrtaucheniidae, Dipluridae, and Nemesiidae. We also elevate five subfamilies to family rank: Anamidae (NEW RANK), Euagridae (NEW RANK), Ischnothelidae (NEW RANK), Pycnothelidae (NEW RANK), and Bemmeridae (NEW RANK). Three families Entypesidae (NEW FAMILY), Microhexuridae (NEW FAMILY), and Stasimopidae (NEW FAMILY), and one subfamily Australothelinae (NEW SUBFAMILY) are newly proposed. Such a major rearrangement in classification, recognizing nine newly established family-level rank taxa, is the largest the group has seen in over three decades. [Biogeography; molecular clocks; phylogenomics; spider web foraging; taxonomy.].
Collapse
Affiliation(s)
- Vera Opatova
- Department of Entomology and Nematology, University of California, 1282 Academic Surge, One Shields Avenue, Davis, CA 95616, USA
| | - Chris A Hamilton
- Department of Entomology, Plant Pathology & Nematology, University of Idaho, 875 Perimeter Dr. MS 2329, Moscow ID 83844-2329, USA
| | - Marshal Hedin
- Department of Biology, LSN 204E, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-4614, USA
| | - Laura Montes De Oca
- Departamento de Ecología y Biología Evolutiva, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, Montevideo 11600, Uruguay
| | - Jiři Král
- Department of Genetics and Microbiology, Faculty of Sciences, Charles University, Viničná 5, Prague 2 128 44, Czech Republic
| | - Jason E Bond
- Department of Entomology and Nematology, University of California, 1282 Academic Surge, One Shields Avenue, Davis, CA 95616, USA
| |
Collapse
|
39
|
Hime PM, Lemmon AR, Lemmon ECM, Prendini E, Brown JM, Thomson RC, Kratovil JD, Noonan BP, Pyron RA, Peloso PLV, Kortyna ML, Keogh JS, Donnellan SC, Mueller RL, Raxworthy CJ, Kunte K, Ron SR, Das S, Gaitonde N, Green DM, Labisko J, Che J, Weisrock DW. Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life. Syst Biol 2021; 70:49-66. [PMID: 32359157 PMCID: PMC7823230 DOI: 10.1093/sysbio/syaa034] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 11/30/2022] Open
Abstract
Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree-species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree-species tree discordance; genomics; information theory.].
Collapse
Affiliation(s)
- Paul M Hime
- Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306, USA
| | | | - Elizabeth Prendini
- Division of Vertebrate Zoology: Herpetology, American Museum of Natural History, New York, NY 10024, USA
| | - Jeremy M Brown
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robert C Thomson
- School of Life Sciences, University of Hawai’i, Honolulu, HI 96822, USA
| | - Justin D Kratovil
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
- Department of Entomology, University of Kentucky, Lexington, KY 40546, USA
| | - Brice P Noonan
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Pedro L V Peloso
- Division of Vertebrate Zoology: Herpetology, American Museum of Natural History, New York, NY 10024, USA
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, 66075-750, Brazil
| | - Michelle L Kortyna
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, 2601, Australia
| | - Stephen C Donnellan
- South Australian Museum, North Terrace, Adelaide 5000, Australia
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | | | - Christopher J Raxworthy
- Division of Vertebrate Zoology: Herpetology, American Museum of Natural History, New York, NY 10024, USA
| | - Krushnamegh Kunte
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Santiago R Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Sandeep Das
- Forest Ecology and Biodiversity Conservation Division, Kerala Forest Research Institute, Peechi, Kerala 680653, India
| | - Nikhil Gaitonde
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - David M Green
- Redpath Museum, McGill University, Montreal, Quebec H3A 0C4, Canada
| | - Jim Labisko
- The Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, The University of Kent, Canterbury, Kent, CT2 7NR, UK
- Island Biodiversity and Conservation Centre, University of Seychelles, PO Box 1348, Anse Royale, Mahé, Seychelles
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| |
Collapse
|
40
|
Ballesteros JA, Hormiga G. Molecular phylogeny of the orb-weaving spider genus Leucauge and the intergeneric relationships of Leucauginae (Araneae, Tetragnathidae). INVERTEBR SYST 2021. [DOI: 10.1071/is21029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The tetragnathid genus Leucauge includes some of the most common orb-weaving spiders in the tropics. Although some species in this genus have attained relevance as model systems for several aspects of spider biology, our understanding of the generic diversity and evolutionary relationships among the species is poor. In this study we present the first attempt to determine the phylogenetic structure within Leucauge and the relationship of this genus with other genera of Leucauginae. This is based on DNA sequences from the five loci commonly used and Histone H4, used for the first time in spider phylogenetics. We also assess the informativeness of the standard markers and test for base composition biases in the dataset. Our results suggest that Leucauge is not monophyletic since species of the genera Opas, Opadometa, Mecynometa and Alcimosphenus are included within the current circumscription of the genus. Based on a phylogenetic re-circumscription of the genus to fulfil the requirement for monophyly of taxa, Leucauge White, 1841 is deemed to be a senior synonym of the genera Opas Pickard-Cambridge, 1896 revalidated synonymy, Mecynometa Simon, 1894 revalidated synonymy, Opadometa Archer, 1951 new synonymy and Alcimosphenus Simon, 1895 new synonymy. We identify groups of taxa critical for resolving relationships within Leucauginae and describe the limitations of the standard loci for accomplishing these resolutions.
Collapse
|
41
|
Hebets EA, Bern M, McGinley RH, Roberts A, Kershenbaum A, Starrett J, Bond JE. Sister species diverge in modality-specific courtship signal form and function. Ecol Evol 2021; 11:852-871. [PMID: 33520171 PMCID: PMC7820158 DOI: 10.1002/ece3.7089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/01/2020] [Accepted: 11/05/2020] [Indexed: 12/26/2022] Open
Abstract
Understanding the relative importance of different sources of selection (e.g., the environment, social/sexual selection) on the divergence or convergence of reproductive communication can shed light on the origin, maintenance, or even disappearance of species boundaries. Using a multistep approach, we tested the hypothesis that two presumed sister species of wolf spider with overlapping ranges and microhabitat use, yet differing degrees of sexual dimorphism, have diverged in their reliance on modality-specific courtship signaling. We predicted that male Schizocosa crassipalpata (no ornamentation) rely predominantly on diet-dependent vibratory signaling for mating success. In contrast, we predicted that male S. bilineata (black foreleg brushes) rely on diet-dependent visual signaling. We first tested and corroborated the sister-species relationship between S. crassipalpata and S. bilineata using phylogenomic scale data. Next, we tested for species-specific, diet-dependent vibratory and visual signaling by manipulating subadult diet and subsequently quantifying adult morphology and mature male courtship signals. As predicted, vibratory signal form was diet-dependent in S. crassipalpata, while visual ornamentation (brush area) was diet-dependent in S. bilineata. We then compared the species-specific reliance on vibratory and visual signaling by recording mating across artificially manipulated signaling environments (presence/absence of each modality in a 2 × 2 full factorial design). In accordance with our diet dependence results for S. crassipalpata, the presence of vibratory signaling was important for mating success. In contrast, the light and vibratory environment interacted to influence mating success in S. bilineata, with vibratory signaling being important only in the absence of light. We found no differences in overall activity patterns. Given that these species overlap in much of their range and microhabitat use, we suggest that competition for signaling space may have led to the divergence and differential use of sensory modalities between these sister species.
Collapse
Affiliation(s)
| | - Mitch Bern
- University of Nebraska‐LincolnLincolnNEUSA
| | | | - Andy Roberts
- The Ohio State University at Newark CampusNewarkOHUSA
| | | | | | | |
Collapse
|
42
|
Ospina OE, Tieu L, Apodaca JJ, Lemmon EM. Hidden Diversity in the Mountain Chorus Frog (Pseudacris brachyphona) and the Diagnosis of a New Species of Chorus Frog in the Southeastern United States. COPEIA 2020. [DOI: 10.1643/ch2020009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Oscar E. Ospina
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, Florida 32306; (EML) . Send reprint requests to this address
| | - Lynee Tieu
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, Florida 32306; (EML) . Send reprint requests to this address
| | - Joseph J. Apodaca
- Tangled Bank Conservation, 128 Bingham Road, Suite 1150, Asheville, North Carolina 28806;
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, Florida 32306; (EML) . Send reprint requests to this address
| |
Collapse
|
43
|
Sharanowski BJ, Ridenbaugh RD, Piekarski PK, Broad GR, Burke GR, Deans AR, Lemmon AR, Moriarty Lemmon EC, Diehl GJ, Whitfield JB, Hines HM. Phylogenomics of Ichneumonoidea (Hymenoptera) and implications for evolution of mode of parasitism and viral endogenization. Mol Phylogenet Evol 2020; 156:107023. [PMID: 33253830 DOI: 10.1016/j.ympev.2020.107023] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/28/2020] [Accepted: 11/23/2020] [Indexed: 12/26/2022]
Abstract
Ichneumonoidea is one of the most diverse lineages of animals on the planet with >48,000 described species and many more undescribed. Parasitoid wasps of this superfamily are mostly beneficial insects that attack and kill other arthropods and are important for understanding diversification and the evolution of life history strategies related to parasitoidism. Further, some lineages of parasitoids within Ichneumonoidea have acquired endogenous virus elements (EVEs) that are permanently a part of the wasp's genome and benefit the wasp through host immune disruption and behavioral control. Unfortunately, understanding the evolution of viral acquisition, parasitism strategies, diversification, and host immune disruption mechanisms, is deeply limited by the lack of a robust phylogenetic framework for Ichneumonoidea. Here we design probes targeting 541 genes across 91 taxa to test phylogenetic relationships, the evolution of parasitoid strategies, and the utility of probes to capture polydnavirus genes across a diverse array of taxa. Phylogenetic relationships among Ichneumonoidea were largely well resolved with most higher-level relationships maximally supported. We noted codon use biases between the outgroups, Braconidae, and Ichneumonidae and within Pimplinae, which were largely solved through analyses of amino acids rather than nucleotide data. These biases may impact phylogenetic reconstruction and caution for outgroup selection is recommended. Ancestral state reconstructions were variable for Braconidae across analyses, but consistent for reconstruction of idiobiosis/koinobiosis in Ichneumonidae. The data suggest many transitions between parasitoid life history traits across the whole superfamily. The two subfamilies within Ichneumonidae that have polydnaviruses are supported as distantly related, providing strong evidence for two independent acquisitions of ichnoviruses. Polydnavirus capture using our designed probes was only partially successful and suggests that more targeted approaches would be needed for this strategy to be effective for surveying taxa for these viral genes. In total, these data provide a robust framework for the evolution of Ichneumonoidea.
Collapse
Affiliation(s)
| | - Ryan D Ridenbaugh
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA
| | - Patrick K Piekarski
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA; Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - Gavin R Broad
- Department of Life Sciences, the Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Gaelen R Burke
- Department of Entomology, University of Georgia, Athens, GA 30606, USA
| | - Andrew R Deans
- Department of Entomology, Pennsylvania State University, University Park, PA, 16802
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306, USA
| | | | - Gloria J Diehl
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA
| | - James B Whitfield
- Department of Entomology, University of Illinois, Urbana, IL 61801, USA
| | - Heather M Hines
- Department of Entomology, Pennsylvania State University, University Park, PA, 16802; Department of Biology, Pennsylvania State University, University Park, PA, 16802
| |
Collapse
|
44
|
Cai L, Xi Z, Lemmon EM, Lemmon AR, Mast A, Buddenhagen CE, Liu L, Davis CC. The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales. Syst Biol 2020; 70:491-507. [PMID: 33169797 DOI: 10.1093/sysbio/syaa083] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 10/20/2020] [Accepted: 10/28/2020] [Indexed: 12/20/2022] Open
Abstract
The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering plant order Malpighiales. This order includes 9 of the top 10 most unstable nodes in angiosperms, which have been hypothesized to arise from the rapid radiation during the Cretaceous. Here, we show that coalescent-based methods do not resolve the backbone of Malpighiales and concatenation methods yield inconsistent estimations, providing evidence that gene tree heterogeneity is high in this clade. Despite high levels of ILS and gene tree estimation error, our simulations demonstrate that these two factors alone are insufficient to explain the lack of resolution in this order. To explore this further, we examined triplet frequencies among empirical gene trees and discovered some of them deviated significantly from those attributed to ILS and estimation error, suggesting gene flow as an additional and previously unappreciated phenomenon promoting gene tree variation in Malpighiales. Finally, we applied a novel method to quantify the relative contribution of these three primary sources of gene tree heterogeneity and demonstrated that ILS, gene tree estimation error, and gene flow contributed to 10.0$\%$, 34.8$\%$, and 21.4$\%$ of the variation, respectively. Together, our results suggest that a perfect storm of factors likely influence this lack of resolution, and further indicate that recalcitrant phylogenetic relationships like the backbone of Malpighiales may be better represented as phylogenetic networks. Thus, reducing such groups solely to existing models that adhere strictly to bifurcating trees greatly oversimplifies reality, and obscures our ability to more clearly discern the process of evolution. [Coalescent; concatenation; flanking region; hybrid enrichment, introgression; phylogenomics; rapid radiation, triplet frequency.].
Collapse
Affiliation(s)
- Liming Cai
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Zhenxiang Xi
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Emily Moriarty Lemmon
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306, USA
| | - Austin Mast
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Christopher E Buddenhagen
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA
- AgResearch, 10 Bisley Road, Hamilton 3214, New Zealand
| | - Liang Liu
- Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA
| |
Collapse
|
45
|
Kelava S, Mans BJ, Shao R, Moustafa MAM, Matsuno K, Takano A, Kawabata H, Sato K, Fujita H, Ze C, Plantard O, Hornok S, Gao S, Barker D, Barker SC, Nakao R. Phylogenies from mitochondrial genomes of 120 species of ticks: Insights into the evolution of the families of ticks and of the genus Amblyomma. Ticks Tick Borne Dis 2020; 12:101577. [PMID: 33120251 DOI: 10.1016/j.ttbdis.2020.101577] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 08/19/2020] [Indexed: 11/28/2022]
Abstract
The evolution and phylogenetic relationships of the ticks at both the family and genus levels are contested. The genus Amblyomma and its subgenera are in a state of flux; moreover, the relationships among the three tick families are controversial due to conflicting phylogenetic support for different arrangements of the three families of living ticks. With 18 newly sequenced mitochondrial (mt) genomes of ticks included, we executed the largest mt genome phylogenetic study of ticks so far. Phylogenetic trees were inferred from one sea spider mt genome, one horseshoe crab, five mite mt genomes and 146 tick mt genomes from 120 species: 153 mt genomes in total. Sixteen phylogenetic trees were inferred from 10 datasets using both maximum likelihood and Bayesian inference methods. We describe the first novel mt gene-arrangement for the metastriate Ixodidae in Amblyomma (Africaniella) transversale. Also, three unusual partial 16S rRNA gene inserts were found in the mt genome of Haemaphysalis (Alloceraea) kitaokai: we consider the possible role of past genome translocation events in the formation of these inserts. Our phylogenies revealed evidence that: (i) the genus Amblyomma is polyphyletic with respect to Amblyomma (Africaniella) transversale; (ii) the subgenus Aponomma is apparently embedded in the genus Amblyomma; (iii) Haemaphysalis (Segalia) parva and Haemaphysalis (Alloceraea) kitaokai form a clade to the exclusion of other Haemaphysalis species; and (iv) the phylogenetic position of the family Nuttalliellidae is unstable among phylogenies from different datasets.
Collapse
Affiliation(s)
- Samuel Kelava
- Department of Parasitology, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Ben J Mans
- Epidemiology, Parasites and Vectors, Agricultural Research Council - Onderstepoort Veterinary Research, Onderstepoort, 0110, South Africa; The Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, 0110, South Africa; The Department of Life and Consumer Sciences, University of South Africa, Florida, 1709, South Africa
| | - Renfu Shao
- School of Science and Engineering, GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, 4558, Australia
| | | | - Keita Matsuno
- Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, 060-0818, Japan
| | - Ai Takano
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Hiroki Kawabata
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Kozue Sato
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Hiromi Fujita
- Mahara Institute of Medical Acarology, 56-3 Aratano, Anan-shi, Tokushima, 779-1510, Japan
| | - Chen Ze
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, China
| | | | - Sandor Hornok
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, 1078, Hungary
| | - Shan Gao
- College of Life Sciences, Nankai University, Tianjin, PR China
| | - Dayana Barker
- School of Veterinary Science, The University of Queensland, Gatton, Queensland 4343, Australia
| | - Stephen C Barker
- Department of Parasitology, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, 4072, Australia.
| | - Ryo Nakao
- Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, 060-0818, Japan
| |
Collapse
|
46
|
Rose JP, Toledo CAP, Lemmon EM, Lemmon AR, Sytsma KJ. Out of Sight, Out of Mind: Widespread Nuclear and Plastid-Nuclear Discordance in the Flowering Plant Genus Polemonium (Polemoniaceae) Suggests Widespread Historical Gene Flow Despite Limited Nuclear Signal. Syst Biol 2020; 70:162-180. [PMID: 32617587 DOI: 10.1093/sysbio/syaa049] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 06/10/2020] [Accepted: 06/23/2020] [Indexed: 12/13/2022] Open
Abstract
Phylogenomic data from a rapidly increasing number of studies provide new evidence for resolving relationships in recently radiated clades, but they also pose new challenges for inferring evolutionary histories. Most existing methods for reconstructing phylogenetic hypotheses rely solely on algorithms that only consider incomplete lineage sorting (ILS) as a cause of intra- or intergenomic discordance. Here, we utilize a variety of methods, including those to infer phylogenetic networks, to account for both ILS and introgression as a cause for nuclear and cytoplasmic-nuclear discordance using phylogenomic data from the recently radiated flowering plant genus Polemonium (Polemoniaceae), an ecologically diverse genus in Western North America with known and suspected gene flow between species. We find evidence for widespread discordance among nuclear loci that can be explained by both ILS and reticulate evolution in the evolutionary history of Polemonium. Furthermore, the histories of organellar genomes show strong discordance with the inferred species tree from the nuclear genome. Discordance between the nuclear and plastid genome is not completely explained by ILS, and only one case of discordance is explained by detected introgression events. Our results suggest that multiple processes have been involved in the evolutionary history of Polemonium and that the plastid genome does not accurately reflect species relationships. We discuss several potential causes for this cytoplasmic-nuclear discordance, which emerging evidence suggests is more widespread across the Tree of Life than previously thought. [Cyto-nuclear discordance, genomic discordance, phylogenetic networks, plastid capture, Polemoniaceae, Polemonium, reticulations.].
Collapse
Affiliation(s)
- Jeffrey P Rose
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Biology, University of Nebraska at Kearney, Kearney, NE 68849, USA
| | - Cassio A P Toledo
- Programa de Pós-Graduação em Biologia Vegetal, Instituto de Biolgia, Universidade Estadual de Campinas-UNICAMP, Rua Monteiro Lobato, 255, Campinas, SP. CEP: 13083-862, Brazil
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306, USA
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA
| |
Collapse
|
47
|
Garrison NL, Brewer MS, Bond JE. Shifting evolutionary sands: transcriptome characterization of the Aptostichus atomarius species complex. BMC Evol Biol 2020; 20:68. [PMID: 32539685 PMCID: PMC7294663 DOI: 10.1186/s12862-020-01606-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/20/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mygalomorph spiders represent a diverse, yet understudied lineage for which genomic level data has only recently become accessible through high-throughput genomic and transcriptomic sequencing methods. The Aptostichus atomarius species complex (family Euctenizidae) includes two coastal dune endemic members, each with inland sister species - affording exploration of dune adaptation associated patterns at the transcriptomic level. We apply an RNAseq approach to examine gene family conservation across the species complex and test for patterns of positive selection along branches leading to dune endemic species. RESULTS An average of ~ 44,000 contigs were assembled for eight spiders representing dune (n = 2), inland (n = 4), and atomarius species complex outgroup taxa (n = 2). Transcriptomes were estimated to be 64% complete on average with 77 spider reference orthologs missing from all taxa. Over 18,000 orthologous gene clusters were identified within the atomarius complex members, > 5000 were detected in all species, and ~ 4700 were shared between species complex members and outgroup Aptostichus species. Gene family analysis with the FUSTr pipeline identified 47 gene families appearing to be under selection in the atomarius ingroup; four of the five top clusters include sequences strongly resembling other arthropod venom peptides. The COATS pipeline identified six gene clusters under positive selection on branches leading to dune species, three of which reflected the preferred species tree. Genes under selection were identified as Cytochrome P450 2c15 (also recovered in the FUSTr analysis), Niemann 2 Pick C1-like, and Kainate 2 isoform X1. CONCLUSIONS We have generated eight draft transcriptomes for a closely related and ecologically diverse group of trapdoor spiders, identifying venom gene families potentially under selection across the Aptostichus atomarius complex and chemosensory-associated gene families under selection in dune endemic lineages.
Collapse
Affiliation(s)
- Nicole L. Garrison
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, 203 Swingle Hall, Auburn, AL 36849 USA
| | - Michael S. Brewer
- Department of Biology, East Carolina University, Howell Science Complex N407, 1000 E 5th St, Greenville, NC 27858 USA
| | - Jason E. Bond
- Department of Entomology and Nematology, University of California Davis, Academic Surge Building 1282, Davis, CA 95616-5270 USA
| |
Collapse
|
48
|
Crowl AA, Manos PS, McVay JD, Lemmon AR, Lemmon EM, Hipp AL. Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus). THE NEW PHYTOLOGIST 2020; 226:1158-1170. [PMID: 30963585 DOI: 10.1111/nph.15842] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/29/2019] [Indexed: 05/10/2023]
Abstract
Botanists have long recognised interspecific gene flow as a common occurrence within white oaks (Quercus section Quercus). Historical allele exchange, however, has not been fully characterised and the complex genomic signals resulting from the combination of vertical and horizontal gene transmission may confound phylogenetic inference and obscure our ability to accurately infer the deep evolutionary history of oaks. Using anchored enrichment, we obtained a phylogenomic dataset consisting of hundreds of single-copy nuclear loci. Concatenation, species-tree and network analyses were carried out in an attempt to uncover the genomic signal of ancient introgression and infer the divergent phylogenetic topology for the white oak clade. Locus and site-level likelihood comparisons were then conducted to further explore the introgressed signal within our dataset. Historical, intersectional gene flow is suggested to have occurred between an ancestor of the Eurasian Roburoid lineage and Quercus pontica and North American Dumosae and Prinoideae lineages. Despite extensive time past, our approach proved successful in detecting the genomic signature of ancient introgression. Our results, however, highlight the importance of sampling and the use of a plurality of analytical tools and methods to sufficiently explore genomic datasets, uncover this signal, and accurately infer evolutionary history.
Collapse
Affiliation(s)
- Andrew A Crowl
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Paul S Manos
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - John D McVay
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, 32317, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 89 Chieftan Way, Tallahassee, FL, 32317, USA
| | - Andrew L Hipp
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL, 60532, USA
- The Field Museum, 1400 S Lake Shore Drive, Chicago, IL, 60605, USA
| |
Collapse
|
49
|
Pyron RA, O'Connell KA, Lemmon EM, Lemmon AR, Beamer DA. Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus). Mol Phylogenet Evol 2020; 146:106751. [DOI: 10.1016/j.ympev.2020.106751] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 01/02/2020] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
|
50
|
Novikova PY, Brennan IG, Booker W, Mahony M, Doughty P, Lemmon AR, Moriarty Lemmon E, Roberts JD, Yant L, Van de Peer Y, Keogh JS, Donnellan SC. Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus. PLoS Genet 2020; 16:e1008769. [PMID: 32392206 PMCID: PMC7259803 DOI: 10.1371/journal.pgen.1008769] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 05/29/2020] [Accepted: 04/08/2020] [Indexed: 01/13/2023] Open
Abstract
Polyploidy has played an important role in evolution across the tree of life but it is still unclear how polyploid lineages may persist after their initial formation. While both common and well-studied in plants, polyploidy is rare in animals and generally less understood. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful animal polyploid model system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin and inheritance mode of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We describe rapid speciation of diploid Neobatrachus species and show that the three independently originated polyploid species have tetrasomic or mixed inheritance. We document higher genetic diversity in tetraploids, resulting from widespread gene flow between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate on differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which correspond to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on the evolution of adaptation in animals.
Collapse
Affiliation(s)
- Polina Yu. Novikova
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Ian G. Brennan
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, Australia
| | - William Booker
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Michael Mahony
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
| | - Paul Doughty
- Western Australian Museum, Welshpool, Perth, Australia
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, Florida, United States of America
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - J. Dale Roberts
- School of Biological Sciences, and, Centre for Evolutionary Biology, University of Western Australia, Albany, Western Australia, Australia
| | - Levi Yant
- School of Life Sciences and Future Food Beacon, University of Nottingham, Nottingham, United Kingdom
| | - Yves Van de Peer
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - J. Scott Keogh
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, Australia
| | - Stephen C. Donnellan
- South Australian Museum, North Terrace, Adelaide, Australia
- School of Biological Sciences, University of Adelaide, North Terrace, Adelaide, Australia
| |
Collapse
|