1
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Myburgh AM, Barnes A, Henriques R, Daniels SR. Congruent patterns of cryptic cladogenesis revealed using RADseq and Sanger sequencing in a velvet worm species complex (Onychophora: Peripatopsidae: Peripatopsis sedgwicki). Mol Phylogenet Evol 2024; 198:108132. [PMID: 38909874 DOI: 10.1016/j.ympev.2024.108132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/24/2024] [Accepted: 06/15/2024] [Indexed: 06/25/2024]
Abstract
In the present study, first generation DNA sequencing (mitochondrial cytochrome c oxidase subunit one, COI) and reduced-representative genomic RADseq data were used to understand the patterns and processes of diversification of the velvet worm, Peripatopsis sedgwicki species complex across its distribution range in South Africa. For the RADseq data, three datasets (two primary and one supplementary) were generated corresponding to 1,259-11,468 SNPs, in order to assess the diversity and phylogeography of the species complex. Tree topologies for the two primary datasets were inferred using maximum likelihood and Bayesian inferences methods. Phylogenetic analyses using the COI datasets retrieved four distinct, well-supported clades within the species complex. Five species delimitation methods applied to the COI data (ASAP, bPTP, bGMYC, STACEY and iBPP) all showed support for the distinction of the Fort Fordyce Nature Reserve specimens. In the main P. sedgwicki species complex, the species delimitation methods revealed a variable number of operational taxonomic units and overestimated the number of putative taxa. Divergence time estimates coupled with the geographic exclusivity of species and phylogeographic results suggest recent cladogenesis during the Plio/Pleistocene. The RADseq data were subjected to a principal components analysis and a discriminant analysis of principal components, under a maximum-likelihood framework. The latter results corroborate the four main clades observed using the COI data, however, applying additional filtering revealed additional diversity. The high overall congruence observed between the RADseq data and COI data suggest that first generation sequence data remain a cheap and effective method for evolutionary studies, although RADseq does provide a far greater resolution of contemporary temporo-spatial patterns.
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Affiliation(s)
- Angus Macgregor Myburgh
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, 7602, South Africa
| | - Aaron Barnes
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, 7602, South Africa
| | - Romina Henriques
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, South Africa
| | - Savel R Daniels
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, 7602, South Africa.
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2
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Karcher MD, Zhang C, Matsen FA. Variational Supertrees for Bayesian Phylogenetics. Bull Math Biol 2024; 86:114. [PMID: 39101994 DOI: 10.1007/s11538-024-01338-5] [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: 11/23/2022] [Accepted: 06/27/2024] [Indexed: 08/06/2024]
Abstract
Bayesian phylogenetic inference is powerful but computationally intensive. Researchers may find themselves with two phylogenetic posteriors on overlapping data sets and may wish to approximate a combined result without having to re-run potentially expensive Markov chains on the combined data set. This raises the question: given overlapping subsets of a set of taxa (e.g. species or virus samples), and given posterior distributions on phylogenetic tree topologies for each of these taxon sets, how can we optimize a probability distribution on phylogenetic tree topologies for the entire taxon set? In this paper we develop a variational approach to this problem and demonstrate its effectiveness. Specifically, we develop an algorithm to find a suitable support of the variational tree topology distribution on the entire taxon set, as well as a gradient-descent algorithm to minimize the divergence from the restrictions of the variational distribution to each of the given per-subset probability distributions, in an effort to approximate the posterior distribution on the entire taxon set.
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Affiliation(s)
- Michael D Karcher
- Department of Math & CS, Muhlenberg College, 2400 W Chew St, Allentown, PA, 18104, USA.
- Computational Biology Program, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, 98109, USA.
| | - Cheng Zhang
- School of Mathematical Sciences and Center for Statistical Science, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871, People's Republic of China
| | - Frederic A Matsen
- Computational Biology Program, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, 98109, USA
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3
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Zhang Y, Wang J, Yu J. PSA: an effective method for predicting horizontal gene transfers through parsimonious phylogenetic networks. Cladistics 2024; 40:443-455. [PMID: 38717786 DOI: 10.1111/cla.12578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 03/08/2024] [Accepted: 03/20/2024] [Indexed: 07/15/2024] Open
Abstract
Horizontal gene transfer (HGT) from one organism to another, according to some researchers, can be abundant in the evolution of species. A phylogenetic network is a network structure that describes the HGTs among species. Several studies have proposed methods to construct phylogenetic networks to predict HGTs based on parsimony values. Existing definitions of parsimony values for a phylogenetic network are based on the assumption that each gene site or segment evolves independently along different trees in the network. However, in the current study, we define a novel parsimony value, denoted the p definition, for phylogenetic networks, considering that a gene as a whole typically evolves along a tree. Using Simulated Annealing, a new method called the Phylogeny with Simulated Annealing (PSA) algorithm is proposed to search for an optimal network based on the p definition. The PSA method is tested on the simulated data. The results reveal that the parsimonious networks constructed using PSA can better represent the evolutionary relationships of species involving HGTs. Additionally, the HGTs predicted using PSA are more accurate than those predicted using other methods. The PSA algorithm is publicly accessible at http://github.com/imustu/sap.
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Affiliation(s)
- Yuan Zhang
- School of Computer Science, Inner Mongolia University, Hohhot, 010021, China
| | - Juan Wang
- School of Computer Science, Inner Mongolia University, Hohhot, 010021, China
| | - Jing Yu
- College of Education, Inner Mongolia Normal University, Hohhot, 010022, China
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4
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Mbewe W, Mukasa S, Ochwo-Ssemakula M, Sseruwagi P, Tairo F, Ndunguru J, Duffy S. Cassava brown streak virus evolves with a nucleotide-substitution rate that is typical for the family Potyviridae. Virus Res 2024; 346:199397. [PMID: 38750679 PMCID: PMC11145536 DOI: 10.1016/j.virusres.2024.199397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 05/08/2024] [Accepted: 05/12/2024] [Indexed: 05/25/2024]
Abstract
The ipomoviruses (family Potyviridae) that cause cassava brown streak disease (cassava brown streak virus [CBSV] and Uganda cassava brown streak virus [UCBSV]) are damaging plant pathogens that affect the sustainability of cassava production in East and Central Africa. However, little is known about the rate at which the viruses evolve and when they emerged in Africa - which inform how easily these viruses can host shift and resist RNAi approaches for control. We present here the rates of evolution determined from the coat protein gene (CP) of CBSV (Temporal signal in a UCBSV dataset was not sufficient for comparable analysis). Our BEAST analysis estimated the CBSV CP evolves at a mean rate of 1.43 × 10-3 nucleotide substitutions per site per year, with the most recent common ancestor of sampled CBSV isolates existing in 1944 (95% HPD, between years 1922 - 1963). We compared the published measured and estimated rates of evolution of CPs from ten families of plant viruses and showed that CBSV is an average-evolving potyvirid, but that members of Potyviridae evolve more quickly than members of Virgaviridae and the single representatives of Betaflexiviridae, Bunyaviridae, Caulimoviridae and Closteroviridae.
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Affiliation(s)
- Willard Mbewe
- Department of Biological Sciences, Malawi University of Science and Technology, P. O. Box 5196, Limbe, Malawi.
| | - Settumba Mukasa
- School of Agriculture and Environmental Science, Department of Agricultural Production, P. O. Box 7062, Makerere University, Kampala, Uganda
| | - Mildred Ochwo-Ssemakula
- School of Agriculture and Environmental Science, Department of Agricultural Production, P. O. Box 7062, Makerere University, Kampala, Uganda
| | - Peter Sseruwagi
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar es Slaam, Tanzania
| | - Fred Tairo
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar es Slaam, Tanzania
| | - Joseph Ndunguru
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar es Slaam, Tanzania
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, United States.
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5
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Nagata N. Phylogeography of Parnassius citrinarius Based on Mitochondrial DNA Reveals Large Differences in Genetic Structure between the Eastern and Western Japan. Zoolog Sci 2024; 41:385-391. [PMID: 39093284 DOI: 10.2108/zs230072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 04/01/2024] [Indexed: 08/04/2024]
Abstract
The Japanese Archipelago hosts a rich butterfly fauna, and elucidating the genetic structures of multiple species is necessary to clarify their formation processes. This study aimed to reveal the genetic structure and distribution formation process of Parnassius citrinarius, which is widely distributed across the Japanese Archipelago from Hokkaido to Shikoku, through phylogeographic analysis based on the mitochondrial cytochrome c oxidase subunit I (COI) gene sequence. Thirty haplotypes were revealed from 311 individuals from 47 sites, indicating significant differences in the genetic structures between the eastern and western parts of the Japanese Archipelago. In Eastern Japan, multiple genetic clusters were found, with some sites harboring two clusters. The divergence times among populations in Eastern Japan were relatively recent, and no genetic differentiation was observed between regions, including between Hokkaido and Honshu, which are separated by a narrow strait. In contrast, in Western Japan, including Shikoku, unique genetic clusters were observed in each region. The phylogenetic relationships among populations were regionally clustered, and the divergence times were relatively ancient. The distribution and genetic structure of P. citrinarius in the Japanese Archipelago have been significantly influenced by temperature fluctuations and the presence of geographical barriers during the Pleistocene glacial-interglacial cycles, including the potential formation of refugia in Western Japan.
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Affiliation(s)
- Nobuaki Nagata
- Department of Anthropology, National Museum of Nature and Science, Ibaraki 305-0005, Japan,
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6
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Jaito W, Singchat W, Patta C, Thatukan C, Kumnan N, Chalermwong P, Budi T, Panthum T, Wongloet W, Wattanadilokchatkun P, Thong T, Muangmai N, Han K, Duengkae P, Phatcharakullawarawat R, Srikulnath K. Shared alleles and genetic structures in different Thai domestic cat breeds: the possible influence of common racial origins. Genomics Inform 2024; 22:12. [PMID: 39085978 PMCID: PMC11292921 DOI: 10.1186/s44342-024-00013-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 06/24/2024] [Indexed: 08/02/2024] Open
Abstract
Over hundreds of years, cats have been domesticated and selectively bred, resulting in numerous pedigreed breeds expedited by recent cat shows and breeding associations. Concerns have been raised about the limited breeding options and the genetic implications of inbreeding, indicating challenges in maintaining genetic diversity and accurate identification in purebred cats. In this study, genetic variability and structure were examined in 5 Thai domestic cat breeds using 15 microsatellite markers and mitochondrial DNA (mtDNA) D-loop sequencing. In total, 184 samples representing the Wichien Maat (WCM), Suphalak (SL), Khao-Manee (KM), Korat (KR), and Konja (KJ) breeds were analyzed. High genetic diversity (Ho and He > 0.5) was observed in all breeds, and mtDNA analysis revealed two primary haplogroups (A and B) that were shared among all domestic cat breeds in Thailand and globally. However, minor differences were observed between Thai domestic cat breeds based on clustering analyses, in which a distinct genetic structure was observed in the WCM breed. This suggests that allele fixation for distinctive morphological traits has occurred in Thai domestic cat breeds that emerged in isolated regions with shared racial origins. Analysis of relationships among individuals within the breed revealed high identification efficiency in Thai domestic cat breeds (P(ID)sibs < 10-4). Additionally, diverse and effective individual identification can be ensured by optimizing marker efficiency by using only nine loci. This comprehensive genetic characterization provides valuable insights into conservation strategies and breeding practices for Thai domestic cat breeds.
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Grants
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- 6514400931,6514400892, 6514400906, 6514400914, 6514400949 Higher Education for Industry Consortium (Hi-FI)
- FF(S-KU)17.66, FF(SRU)25.64, and FF(KU)45.67 Kasetsart University Research and Development Institute funds
- FF(S-KU)17.66, FF(SRU)25.64, and FF(KU)45.67 Kasetsart University Research and Development Institute funds
- FF(S-KU)17.66, FF(SRU)25.64, and FF(KU)45.67 Kasetsart University Research and Development Institute funds
- FF(S-KU)17.66, FF(SRU)25.64, and FF(KU)45.67 Kasetsart University Research and Development Institute funds
- 3/2564 Thailand Science Research and Innovation (TSRI) grant through the Kasetsart University Reinventing University Program 2021
- 3/2564 Thailand Science Research and Innovation (TSRI) grant through the Kasetsart University Reinventing University Program 2021
- Higher Education for Industry Consortium (Hi–FI)
- International SciKU Branding (ISB), Faculty of Science, Kasetsart University
- High-Quality Research Graduate Development Cooperation Project between Kasetsart University and the National Science and Technology Development Agency (NSTDA)
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Affiliation(s)
- Wattanawan Jaito
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, Bangkok, 10520, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
| | - Chananya Patta
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, Bangkok, 10520, Thailand
| | - Chadaphon Thatukan
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, Bangkok, 10520, Thailand
| | - Nichakorn Kumnan
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, Bangkok, 10520, Thailand
| | - Piangjai Chalermwong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Mind Pets Animal Hospital, 169/10 Khlongsongtonnun, Latkrabang, Bangkok, 10520, Thailand
| | - Trifan Budi
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Wongsathit Wongloet
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Microbiology, Dankook University, Cheonan, 31116, Korea
- Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan, 31116, Korea
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | | | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Sciences for Industry, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok, 10900, Thailand.
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7
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Wong MK, Chen WJ. Exploring the phylogeny and depth evolution of cusk eels and their relatives (Ophidiiformes: Ophidioidei). Mol Phylogenet Evol 2024; 199:108164. [PMID: 39084413 DOI: 10.1016/j.ympev.2024.108164] [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: 11/01/2023] [Revised: 07/27/2024] [Accepted: 07/27/2024] [Indexed: 08/02/2024]
Abstract
With 289 known species in 51 genera, the ophidiiform family Ophidiidae together with their relatives from the Carapidae (36 species in eight genera) of the same suborder Ophidioidei dominate the deep sea, but some occur also in shallow water habitats. Despite their high species diversity in the deep sea and wide bathymetric distributions, their phylogenetic relationships and evolution remain unexplored due in part to sampling difficulties. Thanks to the biodiversity exploratory program entitled "Tropical Deep-Sea Benthos" and joint efforts between Taiwan and French teams for sampling from different localities across the Indo-West Pacific over the last two decades, we are able to compile comprehensive datasets for investigations. In this study, 59 samples representing 36 of 59 known ophidioid genera are selected and used to construct a multi-gene dataset to infer the phylogenetic relationships of ophidioid fishes and their relatives. Our results reveal that the Ophidiidae forms a paraphyletic group with respect to the Carapidae. The four main clades of Ophidioidei resolved are the (1) clade comprising species from the subfamily Brotulinae; (2) clade that includes species in the genera Acanthonus and Xyelacyba; (3) clade grouping Hypopleuron caninum with species from the family Carapidae; and (4) clade containing the species in the subfamily Brotulotaenilinae, Neobythitinae (in part), and Ophidiinae. Accordingly, we suggest the following new revisions based on our results and proposed morphological diagnoses. The subfamily Brotulinae should be elevated to the family level. The genera Xyelacyba and probably Tauredophidium (unsampled in this study) should be included in the newly established family Acanthonidae with Acanthonus. The families Carapidae and Ophidiidae are re-defined. Our time-calibrated phylogenetic and ancestral depth reconstructions enable us to clarify the evolutionary history of ophidiiform fishes and infer past patterns of species distributions at different depths. While Ophidiiformes is inferred to have originated in shallow waters around 96.25 million years ago (Mya), the common ancestor to the Ophidioidei is inferred to have invaded the deep sea around 90.22 Mya, the dates coinciding with the global anoxic event of the OAE2. The observed bathymetric distribution patterns in Ophidioidei most likely point to the mesopelagic zone as the center of origin and diversification. This was followed by multiple events of depth transitions or range expansions towards either shallower waters or greater depth zones, which were likely triggered by past climate changes during the Paleogene-Neogene.
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Affiliation(s)
- Man-Kwan Wong
- Institute of Oceanography, National Taiwan University, No.1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
| | - Wei-Jen Chen
- Institute of Oceanography, National Taiwan University, No.1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
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8
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Wong TKF, Cherryh C, Rodrigo AG, Hahn MW, Minh BQ, Lanfear R. MAST: Phylogenetic Inference with Mixtures Across Sites and Trees. Syst Biol 2024; 73:375-391. [PMID: 38421146 PMCID: PMC11282360 DOI: 10.1093/sysbio/syae008] [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: 09/28/2022] [Revised: 12/18/2023] [Accepted: 02/27/2024] [Indexed: 03/02/2024] Open
Abstract
Hundreds or thousands of loci are now routinely used in modern phylogenomic studies. Concatenation approaches to tree inference assume that there is a single topology for the entire dataset, but different loci may have different evolutionary histories due to incomplete lineage sorting (ILS), introgression, and/or horizontal gene transfer; even single loci may not be treelike due to recombination. To overcome this shortcoming, we introduce an implementation of a multi-tree mixture model that we call mixtures across sites and trees (MAST). This model extends a prior implementation by Boussau et al. (2009) by allowing users to estimate the weight of each of a set of pre-specified bifurcating trees in a single alignment. The MAST model allows each tree to have its own weight, topology, branch lengths, substitution model, nucleotide or amino acid frequencies, and model of rate heterogeneity across sites. We implemented the MAST model in a maximum-likelihood framework in the popular phylogenetic software, IQ-TREE. Simulations show that we can accurately recover the true model parameters, including branch lengths and tree weights for a given set of tree topologies, under a wide range of biologically realistic scenarios. We also show that we can use standard statistical inference approaches to reject a single-tree model when data are simulated under multiple trees (and vice versa). We applied the MAST model to multiple primate datasets and found that it can recover the signal of ILS in the Great Apes, as well as the asymmetry in minor trees caused by introgression among several macaque species. When applied to a dataset of 4 Platyrrhine species for which standard concatenated maximum likelihood (ML) and gene tree approaches disagree, we observe that MAST gives the highest weight (i.e., the largest proportion of sites) to the tree also supported by gene tree approaches. These results suggest that the MAST model is able to analyze a concatenated alignment using ML while avoiding some of the biases that come with assuming there is only a single tree. We discuss how the MAST model can be extended in the future.
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Affiliation(s)
- Thomas K F Wong
- School of Computing, Australian National University, Canberra, ACT 2601, Australia
| | - Caitlin Cherryh
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Allen G Rodrigo
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Matthew W Hahn
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA
| | - Bui Quang Minh
- School of Computing, Australian National University, Canberra, ACT 2601, Australia
| | - Robert Lanfear
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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9
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Leal JL, Milesi P, Hodková E, Zhou Q, James J, Eklund DM, Pyhäjärvi T, Salojärvi J, Lascoux M. Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles. Syst Biol 2024; 73:392-418. [PMID: 38613229 PMCID: PMC11282369 DOI: 10.1093/sysbio/syae012] [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: 08/17/2023] [Revised: 12/18/2023] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Introgression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid's ancestral species, profoundly reshaping the polyploid's genomic composition. In such complex polyploids, it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 178,000-188,000 generations ago. Extensive hybridization with B. pendula, B. nana, and B. humilis followed in the aftermath of autopolyploidization, with the relative contribution of each of these species to the B. pubescens genome varying markedly across the species' range. Functional analysis of B. pubescens loci containing alleles introgressed from B. nana identified multiple genes involved in climate adaptation, while loci containing alleles derived from B. humilis revealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.
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Affiliation(s)
- J Luis Leal
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Pascal Milesi
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, 75237 Uppsala, Sweden
| | - Eva Hodková
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16521 Prague, Czech Republic
| | - Qiujie Zhou
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Jennifer James
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - D Magnus Eklund
- Physiology and Environmental Toxicology, Department of Organismal Biology, Uppsala University, Norbyvägen 18A, 75236 Uppsala, Sweden
| | - Tanja Pyhäjärvi
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, P.O. Box 65 (Viikinkaari 1), 00014 Helsinki, Finland
- Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Jarkko Salojärvi
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, P.O. Box 65 (Viikinkaari 1), 00014 Helsinki, Finland
| | - Martin Lascoux
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, 75237 Uppsala, Sweden
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10
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Wang N, Shan C, Chen D, Hu Y, Sun Y, Wang Y, Liang B, Liang W. "Isolation by Gentes with Asymmetric Migration" shapes the genetic structure of the common cuckoo in China. Integr Zool 2024. [PMID: 38872343 DOI: 10.1111/1749-4877.12853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Amid coevolutionary arms races between brood parasitic birds and their diverse host species, the formation of host-specific races, or gentes, has drawn significant research focus. Nevertheless, numerous questions about gentes evolutionary patterns persist. Here, we investigated the potential for gentes evolution across multiple common cuckoo (Cuculus canorus) populations parasitizing diverse host species in China. Using maternal (mitochondrial and W-linked DNA) and biparental (autosomal and Z-linked DNA) markers, we found consistent clustering of cuckoo gentes (rather than geographical populations) into distinct clades in matrilineal gene trees, indicating robust differentiation. In contrast, biparental markers indicated intermixing of all gentes, suggesting asymmetric gene flow regardless of geography. Unlike the mitonuclear discordance commonly resulting from incomplete lineage sorting, adaptive introgression, or demographic disparities, the observed pattern in brood parasitic cuckoos might reflect biased host preferences between sexes. We hereby present the "Isolation by Gentes with Asymmetric Migration" model. According to this model, the maternal line differentiation of the common cuckoo in China is potentially driven by host preferences in females, whereas males maintained the integrity of the cuckoo species through random mating. To achieve this, cuckoo males could perform flexible migration among gentes or engage in early copulation with females before reaching the breeding sites, allowing female cuckoos to store sperm from various gentes. Future studies collecting additional samples from diverse cuckoo gentes with overlapping distribution and investigating the migratory and copulation patterns of each sex would enhance our understanding of sex-biased differentiation among cuckoo populations in China.
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Affiliation(s)
- Ning Wang
- School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Chengbin Shan
- School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Dan Chen
- School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yunbiao Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yuehua Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Ying Wang
- School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Bin Liang
- School of Life Sciences, Inner Mongolia University, Hohhot, China
- Inner Mongolia Engineering Technology Research Center of Germplasm Resources Conservation and Utilization, Hohhot, China
| | - Wei Liang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
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11
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Tomah AA, Khattak AA, Aldarraji MH, Al-Maidi AAH, Mohany M, Al-Rejaie SS, Ogunyemi SO. Sclerotia degradation by Trichoderma-mycoparasitic; an effective and sustainable trend in the drop lettuce disease control caused by Sclerotinia sclerotiorum. Arch Microbiol 2024; 206:286. [PMID: 38829426 DOI: 10.1007/s00203-024-04014-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 06/05/2024]
Abstract
Controlling the hazard of sclerotia produced by the Sclerotinia sclerotiorum is very complex, and it is urgent to adopt an effective method that is harmonious environmentally to control the disease. Among the six isolates isolated from the rhizosphere of lettuce, the isolate HZA84 demonstrated a high activity in its antagonism towards Sclerotinia sclerotiorum in vitro, and produces siderophore. By amplification of internal transcribed spacer (ITS), translation elongation factor 1-alpha (TEF1-α), and RNA polymerase II subunit (RPB2) genes, the isolate HZA84 was identified as Trichoderma asperellum, which was confirmed by analysis of phylogenetic tree. The Scanning electron microscope monitoring detected that the isolate HZA84 spread over the sclerotial surface, thus, damaging, decomposing, and distorting the globular cells of the outer cortex of the sclerotia. The Real-time polymerase chain reaction (RT-qPCR) analysis disclosed the overexpression of two genes (chit33 and chit37) encoding the endochitinase in addition to one gene (prb1) encoding the proteinase during 4 and 8 days of the parasitism behavior of isolate HZA84 on the sclerotia surface. These enzymes aligned together in the sclerotia destruction by hyperparasitism. On the other hand, the pots trial revealed that spraying of isolate HZA84 reduced the drop disease symptoms of lettuce. The disease severity was decreased by 19.33 and the biocontrol efficiency was increased by 80.67% within the fourth week of inoculation. These findings magnify the unique role of Trichoderma in disrupting the development of plant diseases in sustainable ways.
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Affiliation(s)
- Ali Athafah Tomah
- Plant Protection, College of Agriculture, University of Misan, AL-Amarah, 62001, Iraq.
| | - Arif Ali Khattak
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | | | | | - Mohamed Mohany
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 55760, 11451, Riyadh, Saudi Arabia
| | - Salim S Al-Rejaie
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 55760, 11451, Riyadh, Saudi Arabia
| | - Solabomi Olaitan Ogunyemi
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
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12
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Lin Q, Goldberg EE, Leitner T, Molina-París C, King AA, Romero-Severson EO. The Number and Pattern of Viral Genomic Reassortments are not Necessarily Identifiable from Segment Trees. Mol Biol Evol 2024; 41:msae078. [PMID: 38648521 PMCID: PMC11152448 DOI: 10.1093/molbev/msae078] [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: 09/20/2023] [Revised: 02/23/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
Reassortment is an evolutionary process common in viruses with segmented genomes. These viruses can swap whole genomic segments during cellular co-infection, giving rise to novel progeny formed from the mixture of parental segments. Since large-scale genome rearrangements have the potential to generate new phenotypes, reassortment is important to both evolutionary biology and public health research. However, statistical inference of the pattern of reassortment events from phylogenetic data is exceptionally difficult, potentially involving inference of general graphs in which individual segment trees are embedded. In this paper, we argue that, in general, the number and pattern of reassortment events are not identifiable from segment trees alone, even with theoretically ideal data. We call this fact the fundamental problem of reassortment, which we illustrate using the concept of the "first-infection tree," a potentially counterfactual genealogy that would have been observed in the segment trees had no reassortment occurred. Further, we illustrate four additional problems that can arise logically in the inference of reassortment events and show, using simulated data, that these problems are not rare and can potentially distort our observation of reassortment even in small data sets. Finally, we discuss how existing methods can be augmented or adapted to account for not only the fundamental problem of reassortment, but also the four additional situations that can complicate the inference of reassortment.
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Affiliation(s)
- Qianying Lin
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Emma E Goldberg
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Carmen Molina-París
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Aaron A King
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Mathematics, University of Michigan, Ann Arbor, MI, USA
- Center for the Study of Complex Systems, University of Michigan, Ann Arbor, MI, USA
- Santa Fe Institute, Santa Fe, NM, USA
| | - Ethan O Romero-Severson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
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13
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Chen W, Tang Y, Liu T, Hu H, Ou C, Hu Q, Weng Q. Purpureocillium jiangxiense sp. nov.: Entomopathogenic Effects on Ostrinia furnacalis and Galleria mellonella. Microorganisms 2024; 12:1041. [PMID: 38930423 PMCID: PMC11205419 DOI: 10.3390/microorganisms12061041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/10/2024] [Accepted: 05/10/2024] [Indexed: 06/28/2024] Open
Abstract
The genus Purpureocillium is renowned for its role in biocontrol and biotechnological applications. The identification of new species within this genus is crucial for broadening our understanding of its ecological roles and potential utility in sustainable agriculture. This study aimed to characterize a new species of Purpureocillium, isolated from soil in eastern China, and to evaluate its bioactivity against Ostrinia furnacalis (corn moth) and Galleria mellonella (greater wax moth). We utilized morphological characterization; molecular phylogenetic analysis employing ITS, nrLSU, and tef1 genes; and bioactivity assays to identify and characterize the new species. The newly identified species, Purpureocillium jiangxiense sp. nov., displays unique morphological and genetic profiles compared to known species. Bioactivity tests showed that this species exhibits inhibitory effects against O. furnacalis and G. mellonella, highlighting its potential in biocontrol applications. By the ninth day at a spore concentration of 1 × 108 spores/mL, the mortality rate of the corn moth and greater wax moth reached 30% to 50% respectively. The discovery of P. jiangxiense sp. nov. adds to the genetic diversity known within this genus and offers a promising candidate for the development of natural biocontrol agents. It underscores the importance of continued biodiversity exploration and the potential for natural solutions in pest and disease management.
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Affiliation(s)
| | | | | | | | | | - Qiongbo Hu
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou 510642, China; (W.C.); (Y.T.); (T.L.); (H.H.); (C.O.)
| | - Qunfang Weng
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou 510642, China; (W.C.); (Y.T.); (T.L.); (H.H.); (C.O.)
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14
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Diamantidis D, Fan WTL, Birkner M, Wakeley J. Bursts of coalescence within population pedigrees whenever big families occur. Genetics 2024; 227:iyae030. [PMID: 38408329 DOI: 10.1093/genetics/iyae030] [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: 01/23/2024] [Revised: 01/23/2024] [Accepted: 02/18/2024] [Indexed: 02/28/2024] Open
Abstract
We consider a simple diploid population-genetic model with potentially high variability of offspring numbers among individuals. Specifically, against a backdrop of Wright-Fisher reproduction and no selection, there is an additional probability that a big family occurs, meaning that a pair of individuals has a number of offspring on the order of the population size. We study how the pedigree of the population generated under this model affects the ancestral genetic process of a sample of size two at a single autosomal locus without recombination. Our population model is of the type for which multiple-merger coalescent processes have been described. We prove that the conditional distribution of the pairwise coalescence time given the random pedigree converges to a limit law as the population size tends to infinity. This limit law may or may not be the usual exponential distribution of the Kingman coalescent, depending on the frequency of big families. But because it includes the number and times of big families, it differs from the usual multiple-merger coalescent models. The usual multiple-merger coalescent models are seen as describing the ancestral process marginal to, or averaging over, the pedigree. In the limiting ancestral process conditional on the pedigree, the intervals between big families can be modeled using the Kingman coalescent but each big family causes a discrete jump in the probability of coalescence. Analogous results should hold for larger samples and other population models. We illustrate these results with simulations and additional analysis, highlighting their implications for inference and understanding of multilocus data.
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Affiliation(s)
| | - Wai-Tong Louis Fan
- Department of Mathematics, Indiana University, Bloomington, IN 47405, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Matthias Birkner
- Institut für Mathematik, Johannes-Gutenberg-Universität, 55099 Mainz, Germany
| | - John Wakeley
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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15
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Arasti S, Tabaghi P, Tabatabaee Y, Mirarab S. Branch Length Transforms using Optimal Tree Metric Matching. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.13.566962. [PMID: 38746464 PMCID: PMC11092445 DOI: 10.1101/2023.11.13.566962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The abundant discordance between evolutionary relationships across the genome has rekindled interest in ways of comparing and averaging trees on a shared leaf set. However, most attempts at reconciling trees have focused on tree topology, producing metrics for comparing topologies and methods for computing median tree topologies. Using branch lengths, however, has been more elusive, due to several challenges. Species tree branch lengths can be measured in many units, often different from gene trees. Moreover, rates of evolution change across the genome, the species tree, and specific branches of gene trees. These factors compound the stochasticity of coalescence times. Thus, branch lengths are highly heterogeneous across both the genome and the tree. For many downstream applications in phylogenomic analyses, branch lengths are as important as the topology, and yet, existing tools to compare and combine weighted trees are limited. In this paper, we make progress on the question of mapping one tree to another, incorporating both topology and branch length. We define a series of computational problems to formalize finding the best transformation of one tree to another while maintaining its topology and other constraints. We show that all these problems can be solved in quadratic time and memory using a linear algebraic formulation coupled with dynamic programming preprocessing. Our formulations lead to convex optimization problems, with efficient and theoretically optimal solutions. While many applications can be imagined for this framework, we apply it to measure species tree branch lengths in the unit of the expected number of substitutions per site while allowing divergence from ultrametricity across the tree. In these applications, our method matches or surpasses other methods designed directly for solving those problems. Thus, our approach provides a versatile toolkit that finds applications in similar evolutionary questions. Code availability The software is available at https://github.com/shayesteh99/TCMM.git . Data availability Data are available on Github https://github.com/shayesteh99/TCMM-Data.git .
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16
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Bouckaert RR. Variational Bayesian phylogenies through matrix representation of tree space. PeerJ 2024; 12:e17276. [PMID: 38699195 PMCID: PMC11064865 DOI: 10.7717/peerj.17276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 04/01/2024] [Indexed: 05/05/2024] Open
Abstract
In this article, we study the distance matrix as a representation of a phylogeny by way of hierarchical clustering. By defining a multivariate normal distribution on (a subset of) the entries in a matrix, this allows us to represent a distribution over rooted time trees. Here, we demonstrate tree distributions can be represented accurately this way for a number of published tree distributions. Though such a representation does not map to unique trees, restriction to a subspace, in particular one we call a "cube", makes the representation bijective at the cost of not being able to represent all possible trees. We introduce an algorithm "cubeVB" specifically for cubes and show through well calibrated simulation study that it is possible to recover parameters of interest like tree height and length. Although a cube cannot represent all of tree space, it is a great improvement over a single summary tree, and it opens up exciting new opportunities for scaling up Bayesian phylogenetic inference. We also demonstrate how to use a matrix representation of a tree distribution to get better summary trees than commonly used maximum clade credibility trees. An open source implementation of the cubeVB algorithm is available from https://github.com/rbouckaert/cubevb as the cubevb package for BEAST 2.
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Affiliation(s)
- Remco R. Bouckaert
- School of Computer Science, University of Auckland, Auckland, New Zealand
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17
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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.
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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
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18
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Dufresnes C, Monod-Broca B, Bellati A, Canestrelli D, Ambu J, Wielstra B, Dubey S, Crochet PA, Denoël M, Jablonski D. Piecing the barcoding puzzle of Palearctic water frogs (Pelophylax) sheds light on amphibian biogeography and global invasions. GLOBAL CHANGE BIOLOGY 2024; 30:e17180. [PMID: 38465701 DOI: 10.1111/gcb.17180] [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: 10/17/2023] [Revised: 01/04/2024] [Accepted: 01/11/2024] [Indexed: 03/12/2024]
Abstract
Palearctic water frogs (genus Pelophylax) are an outstanding model in ecology and evolution, being widespread, speciose, either threatened or threatening to other species through biological invasions, and capable of siring hybrid offspring that escape the rules of sexual reproduction. Despite half a century of genetic research and hundreds of publications, the diversity, systematics and biogeography of Pelophylax still remain highly confusing, in no small part due to a lack of correspondence between studies. To provide a comprehensive overview, we gathered >13,000 sequences of barcoding genes from >1700 native and introduced localities and built multigene mitochondrial (~17 kb) and nuclear (~10 kb) phylogenies. We mapped all currently recognized taxa and their phylogeographic lineages (>40) to get a grasp on taxonomic issues, cyto-nuclear discordances, the genetic makeup of hybridogenetic hybrids, and the origins of introduced populations. Competing hypotheses for the molecular calibration were evaluated through plausibility tests, implementing a new approach relying on predictions from the anuran speciation continuum. Based on our timetree, we propose a new biogeographic paradigm for the Palearctic since the Paleogene, notably by attributing a prominent role to the dynamics of the Paratethys, a vast paleo-sea that extended over most of Europe. Furthermore, our results show that distinct marsh frog lineages from Eastern Europe, the Balkans, the Near East, and Central Asia (P. ridibundus ssp.) are naturally capable of inducing hybridogenesis with pool frogs (P. lessonae). We identified 14 alien lineages (mostly of P. ridibundus) over ~20 areas of invasions, especially in Western Europe, with genetic signatures disproportionally pointing to the Balkans and Anatolia as the regions of origins, in line with exporting records of the frog leg industry and the stocks of pet sellers. Pelophylax thus emerges as one of the most invasive amphibians worldwide, and deserves much higher conservation concern than currently given by the authorities fighting biological invasions.
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Affiliation(s)
- Christophe Dufresnes
- Laboratory of Amphibian Systematics and Evolutionary Research (LASER), College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Benjamin Monod-Broca
- Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Adriana Bellati
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Daniele Canestrelli
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Johanna Ambu
- Laboratory of Amphibian Systematics and Evolutionary Research (LASER), College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Ben Wielstra
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Sylvain Dubey
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Mathieu Denoël
- Laboratory of Ecology and Conservation of Amphibians (LECA), FOCUS, University of Liège, Liège, Belgium
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
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19
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Albrechtová M, Kašparová EŠ, Langrová I, Hart V, Neuhaus B, Jankovská I, Petrtýl M, Magdálek J, Špakulová M. A revision of the trichostrongylid nematode Cooperia Ransom, 1907, from deer game: recent integrative research confirms the existence of the ancient host-specific species Cooperia ventricosa (Rudolphi, 1809). Front Vet Sci 2024; 11:1346417. [PMID: 38389582 PMCID: PMC10881869 DOI: 10.3389/fvets.2024.1346417] [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: 11/29/2023] [Accepted: 01/24/2024] [Indexed: 02/24/2024] Open
Abstract
The trichostrongylid roundworms of the genus Cooperia, which are important in veterinary medicine, currently comprise 19 valid species that parasitize the small intestine of both free-living and domestic ruminants. Only four Cooperia spp. have been reported in Europe, namely C. oncophora, C. punctata, C. curticei and C. pectinata. In 2018-2022, 25 red deer (Cervus elaphus) and 30 sika deer (Cervus nippon) of both sexes and various ages from several remote locations in the Czech Republic were parasitologically examined. Intestinal nematodes of the genus Cooperia were found only in two northern regions. Using the globally recognized key book on trichostrongylid nematodes, they were preliminarily identified as C. pectinata. However, a molecular analysis of cox2 and ITS rDNA gene sequences revealed that Cooperia sp. parasitizing Czech deer is a separate taxon that is more closely related to C. oncophora than to C. pectinata. A subsequent morphological analysis and literature survey confirmed the independence of deer Cooperia sp., which is similar but not identical to bovid C. pectinata. Previous long-term correct identifications of bovid C. pectinata and misidentifications of deer Cooperia species were caused by a fundamental error in the key book mentioned above. Interestingly, the ancient trichostrongylid nematode Strongylus ventricosus from the type host red deer (Cervus elaphus) shot near Greifswald (Germany) was described by Rudolphi in 1809. Rudolphi's type material (one male and four females) was deposited in the Museum für Naturkunde (Berlin). Later, the ancient species S. ventricosus was taken as a synonym for various Cooperia spp. Our current re-examination of the type male indicated that there is a relatively good agreement with our new material from Czech deer regarding the most important characteristics of S. ventricosus (i.e., the shape and size of the male spicules); however, Rudolphi's type material is in rather poor condition. The suggested resurrection of the deer Cooperia sp. in this study as Cooperia ventricosa (Rudolphi, 1809) requires verification by collecting and analyzing new nematode material from the type locality near Greifswald.
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Affiliation(s)
- Martina Albrechtová
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Science Prague, Prague, Czechia
| | - Eva Štefková Kašparová
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Science Prague, Prague, Czechia
| | - Iva Langrová
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Science Prague, Prague, Czechia
| | - Vlastimil Hart
- Department of Game Management and Wildlife Biology, Faculty of Forestry and Wood Sciences, Czech University of Life Science Prague, Prague, Czechia
| | - Birger Neuhaus
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity, Berlin, Germany
| | - Ivana Jankovská
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Science Prague, Prague, Czechia
| | - Miroslav Petrtýl
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Science Prague, Prague, Czechia
| | - Jan Magdálek
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Science Prague, Prague, Czechia
| | - Marta Špakulová
- Institute of Parasitology, Slovak Academy of Sciences, Košice, Slovakia
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20
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Nieto Lawrence JA, Daniels SR. Sample design in biodiversity studies matters: a fine-scale study of Lawrence's velvet worm, Peripatopsis lawrencei (Onychophora: Peripatopsidae), reveals hidden diversity. INVERTEBR SYST 2024; 38:IS23051. [PMID: 38744496 DOI: 10.1071/is23051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/15/2024] [Indexed: 05/16/2024]
Abstract
A fine-scale phylogenetic and phylogeographic analysis of Peripatopsis lawrencei s.l. was conducted with both mitochondrial and nuclear DNA sequence data, using both external morphology and scanning electron microscopy of taxonomically important characters. A total of 119 sequences were used for the mitochondrial cytochrome c oxidase subunit I (COI ) whereas a single representative specimen from each locality was sequenced for the nuclear 18S rRNA locus. Phylogenetic analyses were conducted on the total COI data set and the combined COI + 18S rRNA data set using a Bayesian analysis and maximum likelihood analyses. For the combined DNA sequence data set, a divergence time estimation was further undertaken in BEAST and specimens placed in a phylogenetic framework including all the described Peripatopsis species from South Africa. In addition, a phylogeographic study was conducted exclusively on P. lawrencei s.s. (clade A) using an analysis of molecular variance and haplotype network. Phylogenetic results indicated that, at the Oubos sample locality, two highly distinct genetic lineages were present (clades A and B), whereas a divergence time estimation suggests a Miocene cladogenesis of the novel Oubos lineage. Marked phylogeographic structure was observed for P. lawrencei s.s. (restricted to clade A) across the distribution range with limited maternal dispersal. Morphologically, the two sympatric lineages at Oubos A and B differed in leg pair number, ventral colour and dorsal scale rank counts, as evident from scanning electron microscopy. Our results support the recognition of a distinct species that occurs in sympatry with P. lawrencei s.s. The new species, P. aereus sp. nov. (clade B) is described and the implication for fine-scale taxonomic studies on saproxylic taxa is discussed. ZooBank: urn:lsid:zoobank.org:pub:AB6E0BDA-7B5F-4FD3-A863-BA7C814E278C.
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Affiliation(s)
- Julian A Nieto Lawrence
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Savel R Daniels
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
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21
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Douglas J, Bouckaert R, Carter CW, Wills P. Enzymic recognition of amino acids drove the evolution of primordial genetic codes. Nucleic Acids Res 2024; 52:558-571. [PMID: 38048305 PMCID: PMC10810186 DOI: 10.1093/nar/gkad1160] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/28/2023] [Accepted: 11/20/2023] [Indexed: 12/06/2023] Open
Abstract
How genetic information gained its exquisite control over chemical processes needed to build living cells remains an enigma. Today, the aminoacyl-tRNA synthetases (AARS) execute the genetic codes in all living systems. But how did the AARS that emerged over three billion years ago as low-specificity, protozymic forms then spawn the full range of highly-specific enzymes that distinguish between 22 diverse amino acids? A phylogenetic reconstruction of extant AARS genes, enhanced by analysing modular acquisitions, reveals six AARS with distinct bacterial, archaeal, eukaryotic, or organellar clades, resulting in a total of 36 families of AARS catalytic domains. Small structural modules that differentiate one AARS family from another played pivotal roles in discriminating between amino acid side chains, thereby expanding the genetic code and refining its precision. The resulting model shows a tendency for less elaborate enzymes, with simpler catalytic domains, to activate amino acids that were not synthesised until later in the evolution of the code. The most probable evolutionary route for an emergent amino acid type to establish a place in the code was by recruiting older, less specific AARS, rather than adapting contemporary lineages. This process, retrofunctionalisation, differs from previously described mechanisms through which amino acids would enter the code.
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Affiliation(s)
- Jordan Douglas
- Department of Physics, The University of Auckland, New Zealand
- Centre for Computational Evolution, The University of Auckland, New Zealand
| | - Remco Bouckaert
- Centre for Computational Evolution, The University of Auckland, New Zealand
- School of Computer Science, The University of Auckland, New Zealand
| | - Charles W Carter
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, USA
| | - Peter R Wills
- Department of Physics, The University of Auckland, New Zealand
- Centre for Computational Evolution, The University of Auckland, New Zealand
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22
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Russo CAM, Eyre-Walker A, Katz LA, Gaut BS. Forty Years of Inferential Methods in the Journals of the Society for Molecular Biology and Evolution. Mol Biol Evol 2024; 41:msad264. [PMID: 38197288 PMCID: PMC10763999 DOI: 10.1093/molbev/msad264] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 11/27/2023] [Indexed: 01/11/2024] Open
Abstract
We are launching a series to celebrate the 40th anniversary of the first issue of Molecular Biology and Evolution. In 2024, we will publish virtual issues containing selected papers published in the Society for Molecular Biology and Evolution journals, Molecular Biology and Evolution and Genome Biology and Evolution. Each virtual issue will be accompanied by a perspective that highlights the historic and contemporary contributions of our journals to a specific topic in molecular evolution. This perspective, the first in the series, presents an account of the broad array of methods that have been published in the Society for Molecular Biology and Evolution journals, including methods to infer phylogenies, to test hypotheses in a phylogenetic framework, and to infer population genetic processes. We also mention many of the software implementations that make methods tractable for empiricists. In short, the Society for Molecular Biology and Evolution community has much to celebrate after four decades of publishing high-quality science including numerous important inferential methods.
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Affiliation(s)
- Claudia A M Russo
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA, USA
| | - Brandon S Gaut
- School of Biological Sciences, University of California, Irvine, CA, USA
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23
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Sanderson BJ, Gambhir D, Feng G, Hu N, Cronk QC, Percy DM, Freaner FM, Johnson MG, Smart LB, Keefover-Ring K, Yin T, Ma T, DiFazio SP, Liu J, Olson MS. Phylogenomics reveals patterns of ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives. Syst Biol 2023; 72:1220-1232. [PMID: 37449764 DOI: 10.1093/sysbio/syad042] [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: 09/29/2021] [Revised: 06/02/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023] Open
Abstract
Despite the economic, ecological, and scientific importance of the genera Salix L. (willows) and Populus L. (poplars, cottonwoods, and aspens) Salicaceae, we know little about the sources of differences in species diversity between the genera and of the phylogenetic conflict that often confounds estimating phylogenetic trees. Salix subgenera and sections, in particular, have been difficult to classify, with one recent attempt termed a "spectacular failure" due to a speculated radiation of the subgenera Vetrix and Chamaetia. Here, we use targeted sequence capture to understand the evolutionary history of this portion of the Salicaceae plant family. Our phylogenetic hypothesis was based on 787 gene regions and identified extensive phylogenetic conflict among genes. Our analysis supported some previously described subgeneric relationships and confirmed the polyphyly of others. Using an fbranch analysis, we identified several cases of hybridization in deep branches of the phylogeny, which likely contributed to discordance among gene trees. In addition, we identified a rapid increase in diversification rate near the origination of the Vetrix-Chamaetia clade in Salix. This region of the tree coincided with several nodes that lacked strong statistical support, indicating a possible increase in incomplete lineage sorting due to rapid diversification. The extraordinary level of both recent and ancient hybridization in both Salix and Populus have played important roles in the diversification and diversity in these two genera.
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Affiliation(s)
- Brian J Sanderson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
- Department of Biology, West Virginia University, Morgantown, WV 26506,USA
| | - Diksha Gambhir
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Guanqiao Feng
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Nan Hu
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Quentin C Cronk
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Diana M Percy
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | | | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, New York 14456, USA
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tongming Yin
- Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, Nanjing, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV 26506,USA
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & College of Life Sciences, Sichuan University, Chengdu 610065, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Matthew S Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
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24
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Rahi ML, Mather PB, de Bello Cioffi M, Ezaz T, Hurwood DA. Genomic Basis of Freshwater Adaptation in the Palaemonid Prawn Genus Macrobrachium: Convergent Evolution Following Multiple Independent Colonization Events. J Mol Evol 2023; 91:976-989. [PMID: 38010517 DOI: 10.1007/s00239-023-10149-6] [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: 10/14/2022] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
Adaptation to different salinity environments can enhance morphological and genomic divergence between related aquatic taxa. Species of prawns in the genus Macrobrachium naturally inhabit different osmotic niches and possess distinctive lifecycle traits associated with salinity tolerance. This study was conducted to investigate the patterns of adaptive genomic divergence during freshwater colonization in 34 Macrobrachium species collected from four continents; Australia, Asia, North and South America. Genotyping-by-sequencing (GBS) technique identified 5018 loci containing 82,636 single nucleotide polymorphisms (SNPs) that were used to reconstruct a phylogenomic tree. An additional phylogeny was reconstructed based on 43 candidate genes, previously identified as being potentially associated with freshwater adaptation. Comparison of the two phylogenetic trees revealed contrasting topologies. The GBS tree indicated multiple independent continent-specific invasions into freshwater by Macrobrachium lineages following common marine ancestry, as species with abbreviated larval development (ALD), i.e., species having a full freshwater life history, appeared reciprocally monophyletic within each continent. In contrast, the candidate gene tree showed convergent evolution for all ALD species worldwide, forming a single, well-supported clade. This latter pattern is likely the result of common evolutionary pressures selecting key mutations favored in continental freshwater habitats Results suggest that following multiple independent invasions into continental freshwaters at different evolutionary timescales, Macrobrachium taxa experienced adaptive genomic divergence, and in particular, convergence in the same genomic regions with parallel shifts in specific conserved phenotypic traits, such as evolution of larger eggs with abbreviated larval developmental.
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Affiliation(s)
- Md Lifat Rahi
- Fisheries and Marine Resource Technology Discipline, Khulna University, Khulna, Bangladesh.
| | - Peter B Mather
- Faculty of Science, Queensland University of Technology (QUT), Brisbane, QLD, 4001, Australia
| | - Marcelo de Bello Cioffi
- Department of Genetics and Evolution, Federal University of Sao Carlos, São Carlos, SP, Brazil
| | - Tariq Ezaz
- Institute for Applied Ecology (IAE), University of Canberra (UC), Canberra, ACT, 2617, Australia
| | - David A Hurwood
- Faculty of Science, Queensland University of Technology (QUT), Brisbane, QLD, 4001, Australia
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25
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Osozawa S. Geologically calibrated mammalian tree and its correlation with global events, including the emergence of humans. Ecol Evol 2023; 13:e10827. [PMID: 38116126 PMCID: PMC10728886 DOI: 10.1002/ece3.10827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 10/09/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023] Open
Abstract
A robust timetree for Mammalia was constructed using the time calibration function of BEAST v1.10.4 and MEGA 11. The analysis involved the application of times of the most recent common ancestors, including a total of 19 mammalian fossil calibration ages following Benton et al. (Palaeontologia Electronica, 2015, 1-106) for their minimum ages. Additionally, fossil calibration ages for Gorilla, Pan, and a geologic event calibration age for otters were incorporated. Using these calibration ages, I constructed a geologically calibrated tree that estimates the age of the Homo and Pan splitting to be 5.69 Ma. The tree carries several significant implications. First, after the initial rifting at 120 Ma, the Atlantic Ocean expanded by over 500 km around Chron 34 (84 Ma), and vicariant speciation between Afrotheria (Africa) and Xenarthra (South America) appears to have commenced around 70 Ma. Additionally, ordinal level differentiations began immediately following the K-Pg boundary (66.0 Ma), supporting previous hypothesis that mammalian radiation rapidly filled ecological niches left vacant by non-avian dinosaurs. I constructed a diagram depicting the relationship between base substitution rate and age using an additional function in BEAST v1.10.4. The diagram reveals an exponential increase in the base substitution rate approaching recent times. This increased base substitution rate during the Neogene period may have contributed to the expansion of biodiversity, including the extensive adaptive radiation that led to the evolution of Homo sapiens. One significant driving factor behind this radiation could be attributed to the emergence and proliferation of C4 grasses since 20 Ma. These grasses have played a role in increasing carbon fixation, reducing atmospheric CO2 concentration, inducing global cooling, and initiating Quaternary glacial-interglacial cycles, thereby causing significant climatic changes.
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Affiliation(s)
- Soichi Osozawa
- Faculty of Science, Institute of Geology and PaleontologyTohoku UniversitySendaiJapan
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26
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Tan X, Qi J, Liu Z, Fan P, Liu G, Zhang L, Shen Y, Li J, Roos C, Zhou X, Li M. Phylogenomics Reveals High Levels of Incomplete Lineage Sorting at the Ancestral Nodes of the Macaque Radiation. Mol Biol Evol 2023; 40:msad229. [PMID: 37823401 PMCID: PMC10638670 DOI: 10.1093/molbev/msad229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/06/2023] [Accepted: 10/08/2023] [Indexed: 10/13/2023] Open
Abstract
The genus Macaca includes 23 species assigned into 4 to 7 groups. It exhibits the largest geographic range and represents the most successful example of adaptive radiation of nonhuman primates. However, intrageneric phylogenetic relationships among species remain controversial and have not been resolved so far. In this study, we conducted a phylogenomic analysis on 16 newly generated and 8 published macaque genomes. We found strong evidence supporting the division of this genus into 7 species groups. Incomplete lineage sorting (ILS) was the primary factor contributing to the discordance observed among gene trees; however, we also found evidence of hybridization events, specifically between the ancestral arctoides/sinica and silenus/nigra lineages that resulted in the hybrid formation of the fascicularis/mulatta group. Combined with fossil data, our phylogenomic data were used to establish a scenario for macaque radiation. These findings provide insights into ILS and potential ancient introgression events that were involved in the radiation of macaques, which will lead to a better understanding of the rapid speciation occurring in nonhuman primates.
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Affiliation(s)
- Xinxin Tan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Geneplus-Beijing Institute, Beijing 102206, China
| | - Jiwei Qi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhijin Liu
- College of Life Sciences, Capital Normal University, Beijing 100049, China
| | - Pengfei Fan
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Gaoming Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liye Zhang
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
| | - Ying Shen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Li
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
| | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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27
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Eggertson QA, Rintoul TL, Lévesque CA. Resolving the Globisporangium ultimum ( Pythium ultimum) species complex. Mycologia 2023; 115:768-786. [PMID: 37796448 DOI: 10.1080/00275514.2023.2241980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/25/2023] [Indexed: 10/06/2023]
Abstract
The Globisporangium ultimum (formerly Pythium ultimum) species complex was previously composed of two morphological varieties: var. ultimum and var. sporangiiferum. Prior attempts to resolve this morphology-based species complex using molecular techniques have been inconclusive or conflicting. The increased availability of sequenced genomes and isolates identified as G. ultimum var. ultimum and var. sporangiiferum has allowed us to examine these relationships at a higher resolution and with a broader scope than previously possible. Using comparative genomics, we identified highly variable gene regions and designed primers for four new protein-coding genes for phylogenetics. These were then used alongside three known markers to generate a nuclear multigene genealogy of the species complex. From a collection of 163 isolates belonging to the target taxa, a subset of 29 was chosen to be included in this study (verified with nuclear rDNA internal transcribed spacer 1 [ITS1] and mitochondrial cytochrome c oxidase subunit 1 [cox1] sequences). Seventeen isolates of var. ultimum were selected to be representative of variations in genotype, morphology, and geographic collection location. The 12 isolates of var. sporangiiferum included all available specimens identified either morphologically (in previous studies) or through sequence similarity with ITS1 and cox1. Based on the fulfillment of reciprocal monophyly and observed genealogical concordance under the genealogical concordance phylogenetic species recognition, we determined that the Globisporangium ultimum species complex is composed of four genetically distinct species: Globisporangium ultimum, Globisporangium sporangiiferum, Globisporangium solveigiae, and Globisporangium bothae.
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Affiliation(s)
- Quinn A Eggertson
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, K.W. Neatby Building, Central Experimental Farm, 960 Carling Ave. Ottawa, Ontario, K1A 0C6, Canada
- Department of Biology, Carleton University, 1125 Colonel By Dr., Ottawa, Ontario, K1S 5B6, Canada
| | - Tara L Rintoul
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, K.W. Neatby Building, Central Experimental Farm, 960 Carling Ave. Ottawa, Ontario, K1A 0C6, Canada
| | - C André Lévesque
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, K.W. Neatby Building, Central Experimental Farm, 960 Carling Ave. Ottawa, Ontario, K1A 0C6, Canada
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28
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Ramirez JL, Machado CB, de Mello Affonso PRA, Galetti PM. Speciation in Coastal Basins Driven by Staggered Headwater Captures: Dispersal of a Species Complex, Leporinus bahiensis, as Revealed by Genome-wide SNP Data. Syst Biol 2023; 72:973-983. [PMID: 37260367 PMCID: PMC10627554 DOI: 10.1093/sysbio/syad034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 06/02/2023] Open
Abstract
Past sea level changes and geological instability along watershed boundaries have largely influenced fish distribution across coastal basins, either by dispersal via palaeodrainages now submerged or by headwater captures, respectively. Accordingly, the South American Atlantic coast encompasses several small and isolated drainages that share a similar species composition, representing a suitable model to infer historical processes. Leporinus bahiensis is a freshwater fish species widespread along adjacent coastal basins over narrow continental shelf with no evidence of palaeodrainage connections at low sea level periods. Therefore, this study aimed to reconstruct its evolutionary history to infer the role of headwater captures in the dispersal process. To accomplish this, we employed molecular-level phylogenetic and population structure analyses based on Sanger sequences (5 genes) and genome-wide SNP data. Phylogenetic trees based on Sanger data were inconclusive, but SNPs data did support the monophyletic status of L. bahiensis. Both COI and SNP data revealed structured populations according to each hydrographic basin. Species delimitation analyses revealed from 3 (COI) to 5 (multilocus approach) MOTUs, corresponding to the sampled basins. An intricate biogeographic scenario was inferred and supported by Approximate Bayesian Computation (ABC) analysis. Specifically, a staggered pattern was revealed and characterized by sequential headwater captures from basins adjacent to upland drainages into small coastal basins at different periods. These headwater captures resulted in dispersal throughout contiguous coastal basins, followed by deep genetic divergence among lineages. To decipher such recent divergences, as herein represented by L. bahiensis populations, we used genome-wide SNPs data. Indeed, the combined use of genome-wide SNPs data and ABC method allowed us to reconstruct the evolutionary history and speciation of L. bahiensis. This framework might be useful in disentangling the diversification process in other neotropical fishes subject to a reticulate geological history.
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Affiliation(s)
- Jorge L Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
- Museo de Historia Natural de la Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Carolina B Machado
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | | | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
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29
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Long W, Chen Y, Wei Y, Feng J, Zhou D, Cai B, Qi D, Zhang M, Zhao Y, Li K, Liu YZ, Wang W, Xie J. A newly isolated Trichoderma Parareesei N4-3 exhibiting a biocontrol potential for banana fusarium wilt by Hyperparasitism. FRONTIERS IN PLANT SCIENCE 2023; 14:1289959. [PMID: 37941669 PMCID: PMC10629295 DOI: 10.3389/fpls.2023.1289959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 09/29/2023] [Indexed: 11/10/2023]
Abstract
Banana Fusarium wilt caused by Fusarium oxysporum f. sp. cubense tropical race4 (Foc TR4) is one of the most destructive soil-borne fungal diseases and currently threatens banana production around the world. Until now, there is lack of an effective method to control banana Fusarium wilt. Therefore, it is urgent to find an effective and eco-friendly strategy against the fungal disease. In this study, a strain of Trichoderma sp. N4-3 was isolated newly from the rhizosphere soil of banana plants. The isolate was identified as Trichoderma parareesei through analysis of TEF1 and RPB2 genes as well as morphological characterization. In vitro antagonistic assay demonstrated that strain N4-3 had a broad-spectrum antifungal activity against ten selected phytopathogenic fungi. Especially, it demonstrated a strong antifungal activity against Foc TR4. The results of the dual culture assay indicated that strain N4-3 could grow rapidly during the pre-growth period, occupy the growth space, and secrete a series of cell wall-degrading enzymes upon interaction with Foc TR4. These enzymes contributed to the mycelial and spore destruction of the pathogenic fungus by hyperparasitism. Additionally, the sequenced genome proved that strain N4-3 contained 21 genes encoding chitinase and 26 genes encoding β-1,3-glucanase. The electron microscopy results showed that theses cell wall-degrading enzymes disrupted the mycelial, spore, and cell ultrastructure of Foc TR4. A pot experiment revealed that addition of strain N4-3 significantly reduced the amount of Foc TR4 in the rhizosphere soil of bananas at 60 days post inoculation. The disease index was decreased by 45.00% and the fresh weight was increased by 63.74% in comparison to the control. Hence, Trichoderma parareesei N4-3 will be a promising biological control agents for the management of plant fungal diseases.
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Affiliation(s)
- Weiqiang Long
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yufeng Chen
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Yongzan Wei
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Junting Feng
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Dengbo Zhou
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Bingyu Cai
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Dengfeng Qi
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Miaoyi Zhang
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Yankun Zhao
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Kai Li
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Yong-Zhong Liu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Wei Wang
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jianghui Xie
- National Key Laboratory of Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei, China
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Smith ML, Hahn MW. Phylogenetic inference using generative adversarial networks. Bioinformatics 2023; 39:btad543. [PMID: 37669126 PMCID: PMC10500083 DOI: 10.1093/bioinformatics/btad543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/25/2023] [Accepted: 09/04/2023] [Indexed: 09/07/2023] Open
Abstract
MOTIVATION The application of machine learning approaches in phylogenetics has been impeded by the vast model space associated with inference. Supervised machine learning approaches require data from across this space to train models. Because of this, previous approaches have typically been limited to inferring relationships among unrooted quartets of taxa, where there are only three possible topologies. Here, we explore the potential of generative adversarial networks (GANs) to address this limitation. GANs consist of a generator and a discriminator: at each step, the generator aims to create data that is similar to real data, while the discriminator attempts to distinguish generated and real data. By using an evolutionary model as the generator, we use GANs to make evolutionary inferences. Since a new model can be considered at each iteration, heuristic searches of complex model spaces are possible. Thus, GANs offer a potential solution to the challenges of applying machine learning in phylogenetics. RESULTS We developed phyloGAN, a GAN that infers phylogenetic relationships among species. phyloGAN takes as input a concatenated alignment, or a set of gene alignments, and infers a phylogenetic tree either considering or ignoring gene tree heterogeneity. We explored the performance of phyloGAN for up to 15 taxa in the concatenation case and 6 taxa when considering gene tree heterogeneity. Error rates are relatively low in these simple cases. However, run times are slow and performance metrics suggest issues during training. Future work should explore novel architectures that may result in more stable and efficient GANs for phylogenetics. AVAILABILITY AND IMPLEMENTATION phyloGAN is available on github: https://github.com/meganlsmith/phyloGAN/.
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Affiliation(s)
- Megan L Smith
- Department of Biology, Indiana University, 1001 E 3rd St, Bloomington, IN 47405, United States
| | - Matthew W Hahn
- Department of Biology, Indiana University, 1001 E 3rd St, Bloomington, IN 47405, United States
- Department of Computer Science, Indiana University, 700 N Woodlawn Avenue, Bloomington, IN 47408, United States
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Yan H, Hu Z, Thomas GWC, Edwards SV, Sackton TB, Liu JS. PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree Discordance. Mol Biol Evol 2023; 40:msad195. [PMID: 37665177 PMCID: PMC10540510 DOI: 10.1093/molbev/msad195] [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: 12/23/2022] [Revised: 08/15/2023] [Accepted: 09/01/2023] [Indexed: 09/05/2023] Open
Abstract
An important goal of evolutionary genomics is to identify genomic regions whose substitution rates differ among lineages. For example, genomic regions experiencing accelerated molecular evolution in some lineages may provide insight into links between genotype and phenotype. Several comparative genomics methods have been developed to identify genomic accelerations between species, including a Bayesian method called PhyloAcc, which models shifts in substitution rate in multiple target lineages on a phylogeny. However, few methods consider the possibility of discordance between the trees of individual loci and the species tree due to incomplete lineage sorting, which might cause false positives. Here, we present PhyloAcc-GT, which extends PhyloAcc by modeling gene tree heterogeneity. Given a species tree, we adopt the multispecies coalescent model as the prior distribution of gene trees, use Markov chain Monte Carlo (MCMC) for inference, and design novel MCMC moves to sample gene trees efficiently. Through extensive simulations, we show that PhyloAcc-GT outperforms PhyloAcc and other methods in identifying target lineage-specific accelerations and detecting complex patterns of rate shifts, and is robust to specification of population size parameters. PhyloAcc-GT is usually more conservative than PhyloAcc in calling convergent rate shifts because it identifies more accelerations on ancestral than on terminal branches. We apply PhyloAcc-GT to two examples of convergent evolution: flightlessness in ratites and marine mammal adaptations, and show that PhyloAcc-GT is a robust tool to identify shifts in substitution rate associated with specific target lineages while accounting for incomplete lineage sorting.
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Affiliation(s)
- Han Yan
- Department of Statistics, Harvard University, Cambridge, MA, USA
| | - Zhirui Hu
- Department of Statistics, Harvard University, Cambridge, MA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | | | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - Jun S Liu
- Department of Statistics, Harvard University, Cambridge, MA, USA
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Liu B, Warnow T. Weighted ASTRID: fast and accurate species trees from weighted internode distances. Algorithms Mol Biol 2023; 18:6. [PMID: 37468904 PMCID: PMC10355063 DOI: 10.1186/s13015-023-00230-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/10/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Species tree estimation is a basic step in many biological research projects, but is complicated by the fact that gene trees can differ from the species tree due to processes such as incomplete lineage sorting (ILS), gene duplication and loss (GDL), and horizontal gene transfer (HGT), which can cause different regions within the genome to have different evolutionary histories (i.e., "gene tree heterogeneity"). One approach to estimating species trees in the presence of gene tree heterogeneity resulting from ILS operates by computing trees on each genomic region (i.e., computing "gene trees") and then using these gene trees to define a matrix of average internode distances, where the internode distance in a tree T between two species x and y is the number of nodes in T between the leaves corresponding to x and y. Given such a matrix, a tree can then be computed using methods such as neighbor joining. Methods such as ASTRID and NJst (which use this basic approach) are provably statistically consistent, very fast (low degree polynomial time) and have had high accuracy under many conditions that makes them competitive with other popular species tree estimation methods. In this study, inspired by the very recent work of weighted ASTRAL, we present weighted ASTRID, a variant of ASTRID that takes the branch uncertainty on the gene trees into account in the internode distance. RESULTS Our experimental study evaluating weighted ASTRID typically shows improvements in accuracy compared to the original (unweighted) ASTRID, and shows competitive accuracy against weighted ASTRAL, the state of the art. Our re-implementation of ASTRID also improves the runtime, with marked improvements on large datasets. CONCLUSIONS Weighted ASTRID is a new and very fast method for species tree estimation that typically improves upon ASTRID and has comparable accuracy to weighted ASTRAL, while remaining much faster. Weighted ASTRID is available at https://github.com/RuneBlaze/internode .
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Affiliation(s)
- Baqiao Liu
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL USA
| | - Tandy Warnow
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL USA
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Scheunert A, Lautenschlager U, Ott T, Oberprieler C. Nano-Strainer: A workflow for the identification of single-copy nuclear loci for plant systematic studies, using target capture kits and Oxford Nanopore long reads. Ecol Evol 2023; 13:e10190. [PMID: 37475726 PMCID: PMC10354226 DOI: 10.1002/ece3.10190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/18/2023] [Accepted: 06/01/2023] [Indexed: 07/22/2023] Open
Abstract
In modern plant systematics, target enrichment enables simultaneous analysis of hundreds of genes. However, when dealing with reticulate or polyploidization histories, few markers may suffice, but often are required to be single-copy, a condition that is not necessarily met with commercial capture kits. Also, large genome sizes can render target capture ineffective, so that amplicon sequencing would be preferable; however, knowledge about suitable loci is often missing. Here, we present a comprehensive workflow for the identification of putative single-copy nuclear markers in a genus of interest, by mining a small dataset from target capture using a few representative taxa. The proposed pipeline assesses sequence variability contained in the data from targeted loci and assigns reads to their respective genes, via a combined BLAST/clustering procedure. Cluster consensus sequences are then examined based on four pre-defined criteria presumably indicative for absence of paralogy. This is done by calculating four specialized indices; loci are ranked according to their performance in these indices, and top-scoring loci are considered putatively single- or low copy. The approach can be applied to any probe set. As it relies on long reads, the present contribution also provides template workflows for processing Nanopore-based target capture data. Obtained markers are further tested and then entered into amplicon sequencing. For the detection of possibly remaining paralogy in these data, which might occur in groups with rampant paralogy, we also employ the long-read assembly tool canu. In diploid representatives of the young Compositae genus Leucanthemum, characterized by high levels of polyploidy, our approach resulted in successful amplification of 13 loci. Modifications to remove traces of paralogy were made in seven of these. A species tree from the markers correctly reproduced main relationships in the genus, however, at low resolution. The presented workflow has the potential to valuably support phylogenetic research, for example in polyploid plant groups.
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Affiliation(s)
- Agnes Scheunert
- Evolutionary and Systematic Botany Group, Institute of Plant SciencesUniversity of RegensburgRegensburgGermany
| | - Ulrich Lautenschlager
- Evolutionary and Systematic Botany Group, Institute of Plant SciencesUniversity of RegensburgRegensburgGermany
| | - Tankred Ott
- Evolutionary and Systematic Botany Group, Institute of Plant SciencesUniversity of RegensburgRegensburgGermany
| | - Christoph Oberprieler
- Evolutionary and Systematic Botany Group, Institute of Plant SciencesUniversity of RegensburgRegensburgGermany
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Pérez-Rodríguez R, Domínguez-Domínguez O, Pedraza-Lara C, Rosas-Valdez R, Pérez-Ponce de León G, García-Andrade AB, Doadrio I. Multi-locus phylogeny of the catfish genus Ictalurus Rafinesque, 1820 (Actinopterygii, Siluriformes) and its systematic and evolutionary implications. BMC Ecol Evol 2023; 23:27. [PMID: 37370016 PMCID: PMC10304232 DOI: 10.1186/s12862-023-02134-w] [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: 04/29/2022] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Ictalurus is one of the most representative groups of North American freshwater fishes. Although this group has a well-studied fossil record and has been the subject of several morphological and molecular phylogenetic studies, incomplete taxonomic sampling and insufficient taxonomic studies have produced a rather complex classification, along with intricate patterns of evolutionary history in the genus that are considered unresolved and remain under debate. RESULTS Based on four loci and the most comprehensive taxonomic sampling analyzed to date, including currently recognized species, previously synonymized species, undescribed taxa, and poorly studied populations, this study produced a resolved phylogenetic framework that provided plausible species delimitation and an evolutionary time framework for the genus Ictalurus. CONCLUSIONS Our phylogenetic hypothesis revealed that Ictalurus comprises at least 13 evolutionary units, partially corroborating the current classification and identifying populations that emerge as putative undescribed taxa. The divergence times of the species indicate that the diversification of Ictalurus dates to the early Oligocene, confirming its status as one of the oldest genera within the family Ictaluridae.
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Affiliation(s)
- Rodolfo Pérez-Rodríguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, 58000, Michoacán, México
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, 58000, Michoacán, México
| | - Carlos Pedraza-Lara
- Forensic Science, Medicine School, National Autonomous University of Mexico, Circuito de la investigación científica s/n, Ciudad Universitaria, Coyoacan, 04510, CdMx, Mexico
| | - Rogelio Rosas-Valdez
- Laboratorio de Colecciones Biológicas y Sistemática Molecular, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Av. Preparatoria S/N, Campus Universitario II, Col. Agronómica, Zacatecas, C. P. 98066, México
| | - Gerardo Pérez-Ponce de León
- Instituto de Biología, UNAM, Circuito exterior s/n, Ciudad Universitaria, Coyoacán, C.P. 04510, D.F, México
- Escuela Nacional de Estudios Superiores Unidad Mérida, Universidad Nacional Autónoma de México, Km 4.5 Carretera Mérida-Tetiz, Ucú, Yucatán, México
| | - Ana Berenice García-Andrade
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, 58000, Michoacán, México
- Laboratorio de Macroecología Evolutiva, Red de Biología Evolutiva, Instituto de Ecología, A.C. Carretera antigua a Coatepec 351, El Haya, Xalapa, 91070, Veracruz, México
| | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, c/José Gutiérrez Abascal 2, Madrid, E-28006, España.
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Carneiro J, Sampaio I, Silva-Júnior JDSE, Martins-Junior A, Farias I, Hrbek T, Boubli J, Schneider H. Molecular Evidence Supports Five Lineages within Chiropotes (Pitheciidae, Platyrrhini). Genes (Basel) 2023; 14:1309. [PMID: 37510215 PMCID: PMC10379672 DOI: 10.3390/genes14071309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 07/30/2023] Open
Abstract
Pitheciines have unique dental specializations among New World monkeys that allow them to feed on fruits with hard pericarps, thus playing a major role as seed predators. The three extant pitheciine genera, Pithecia, Cacajao and Chiropotes, are all endemic to the Amazon region. Because of the uncertainties about interspecific relationships, we reviewed the systematics and taxonomy of the genus Chiropotes. The phylogenetic analyses were performed based on Maximum Likelihood and Bayesian Inference, while species delimitation analyses were carried out using multispecies coalescent methods. In addition, we estimated genetic distances, divergence time and the probable ancestral distribution of this genus. Our results support five species of Chiropotes that emerged during the Plio-Pleistocene. Biogeographic estimates suggest that the ancestor of the current Chiropotes species occupied the endemism areas from Rondônia and Tapajós. Later, subsequent radiation and founder effects associated with the formation of the Amazonian basins probably determined the speciation events within Chiropotes.
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Affiliation(s)
- Jeferson Carneiro
- Institute of Coastal Studies, University Campus of Bragança, Federal University of Pará, Belém 66075-110, Pará, Brazil
| | - Iracilda Sampaio
- Institute of Coastal Studies, University Campus of Bragança, Federal University of Pará, Belém 66075-110, Pará, Brazil
| | | | - Antonio Martins-Junior
- Federal Institute of Education, Science and Technology of Pará, Campus Tucuruí, Tucuruí 68455-210, Pará, Brazil
| | - Izeni Farias
- Laboratório de Evolução e Genética Animal, Federal University of Amazonas, Manaus 69067-005, Amazonas, Brazil
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal, Federal University of Amazonas, Manaus 69067-005, Amazonas, Brazil
| | - Jean Boubli
- School of Environment and Life Sciences, University of Salford, Salford M5 4WT, UK
| | - Horacio Schneider
- Institute of Coastal Studies, University Campus of Bragança, Federal University of Pará, Belém 66075-110, Pará, Brazil
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Ji J, Jackson DJ, Leaché AD, Yang Z. Power of Bayesian and Heuristic Tests to Detect Cross-Species Introgression with Reference to Gene Flow in the Tamias quadrivittatus Group of North American Chipmunks. Syst Biol 2023; 72:446-465. [PMID: 36504374 PMCID: PMC10275556 DOI: 10.1093/sysbio/syac077] [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: 12/07/2021] [Revised: 11/15/2022] [Accepted: 12/01/2022] [Indexed: 10/25/2023] Open
Abstract
In the past two decades, genomic data have been widely used to detect historical gene flow between species in a variety of plants and animals. The Tamias quadrivittatus group of North America chipmunks, which originated through a series of rapid speciation events, are known to undergo massive amounts of mitochondrial introgression. Yet in a recent analysis of targeted nuclear loci from the group, no evidence for cross-species introgression was detected, indicating widespread cytonuclear discordance. The study used the heuristic method HYDE to detect gene flow, which may suffer from low power. Here we use the Bayesian method implemented in the program BPP to re-analyze these data. We develop a Bayesian test of introgression, calculating the Bayes factor via the Savage-Dickey density ratio using the Markov chain Monte Carlo (MCMC) sample under the model of introgression. We take a stepwise approach to constructing an introgression model by adding introgression events onto a well-supported binary species tree. The analysis detected robust evidence for multiple ancient introgression events affecting the nuclear genome, with introgression probabilities reaching 63%. We estimate population parameters and highlight the fact that species divergence times may be seriously underestimated if ancient cross-species gene flow is ignored in the analysis. We examine the assumptions and performance of HYDE and demonstrate that it lacks power if gene flow occurs between sister lineages or if the mode of gene flow does not match the assumed hybrid-speciation model with symmetrical population sizes. Our analyses highlight the power of likelihood-based inference of cross-species gene flow using genomic sequence data. [Bayesian test; BPP; chipmunks; introgression; MSci; multispecies coalescent; Savage-Dickey density ratio.].
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Affiliation(s)
- Jiayi Ji
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Donavan J Jackson
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Box 351800, Seattle, WA 98195-1800, USA
| | - Adam D Leaché
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Box 351800, Seattle, WA 98195-1800, USA
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
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Leal JL, Milesi P, Salojärvi J, Lascoux M. Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences. Syst Biol 2023; 72:372-390. [PMID: 36932679 PMCID: PMC10275558 DOI: 10.1093/sysbio/syad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 10/14/2022] [Accepted: 03/10/2023] [Indexed: 03/19/2023] Open
Abstract
Phylogenetic analysis of polyploid hybrid species has long posed a formidable challenge as it requires the ability to distinguish between alleles of different ancestral origins in order to disentangle their individual evolutionary history. This problem has been previously addressed by conceiving phylogenies as reticulate networks, using a two-step phasing strategy that first identifies and segregates homoeologous loci and then, during a second phasing step, assigns each gene copy to one of the subgenomes of an allopolyploid species. Here, we propose an alternative approach, one that preserves the core idea behind phasing-to produce separate nucleotide sequences that capture the reticulate evolutionary history of a polyploid-while vastly simplifying its implementation by reducing a complex multistage procedure to a single phasing step. While most current methods used for phylogenetic reconstruction of polyploid species require sequencing reads to be pre-phased using experimental or computational methods-usually an expensive, complex, and/or time-consuming endeavor-phasing executed using our algorithm is performed directly on the multiple-sequence alignment (MSA), a key change that allows for the simultaneous segregation and sorting of gene copies. We introduce the concept of genomic polarization that, when applied to an allopolyploid species, produces nucleotide sequences that capture the fraction of a polyploid genome that deviates from that of a reference sequence, usually one of the other species present in the MSA. We show that if the reference sequence is one of the parental species, the polarized polyploid sequence has a close resemblance (high pairwise sequence identity) to the second parental species. This knowledge is harnessed to build a new heuristic algorithm where, by replacing the allopolyploid genomic sequence in the MSA by its polarized version, it is possible to identify the phylogenetic position of the polyploid's ancestral parents in an iterative process. The proposed methodology can be used with long-read and short-read high-throughput sequencing data and requires only one representative individual for each species to be included in the phylogenetic analysis. In its current form, it can be used in the analysis of phylogenies containing tetraploid and diploid species. We test the newly developed method extensively using simulated data in order to evaluate its accuracy. We show empirically that the use of polarized genomic sequences allows for the correct identification of both parental species of an allotetraploid with up to 97% certainty in phylogenies with moderate levels of incomplete lineage sorting (ILS) and 87% in phylogenies containing high levels of ILS. We then apply the polarization protocol to reconstruct the reticulate histories of Arabidopsis kamchatica and Arabidopsis suecica, two allopolyploids whose ancestry has been well documented. [Allopolyploidy; Arabidopsis; genomic polarization; homoeologs; incomplete lineage sorting; phasing; polyploid phylogenetics; reticulate evolution.].
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Affiliation(s)
- J Luis Leal
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Pascal Milesi
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, 75237 Uppsala, Sweden
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, P.O. Box 65 (Viikinkaari 1), 00014 Helsinki, Finland
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Martin Lascoux
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, 75237 Uppsala, Sweden
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Monjaraz-Ruedas R, Mendez RW, Hedin M. Species delimitation, biogeography, and natural history of dwarf funnel web spiders (Mygalomorphae, Hexurellidae, Hexurella) from the United States / Mexico borderlands. Zookeys 2023; 1167:109-157. [PMID: 37363739 PMCID: PMC10285686 DOI: 10.3897/zookeys.1167.103463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/29/2023] [Indexed: 06/28/2023] Open
Abstract
The rarely encountered spider genus Hexurella Gertsch & Platnick, 1979 includes some of the smallest mygalomorph spiders in the world, with four poorly known taxa from central and southeastern montane Arizona, southern California, and northern Baja California Norte. At time of description the genus was known from fewer than 20 individuals, with sparse natural history information suggesting a vagrant, web-building, litter-dwelling natural history. Here the first published taxonomic and natural history information for this taxon is provided in more than 50 years, working from extensive new geographic sampling, consideration of male and female morphology, and sequence capture-based nuclear phylogenomics and mitogenomics. Several new species are easily diagnosed based on distinctive male morphologies, while a complex of populations from central and northern Arizona required an integrative combination of genomic algorithmic species delimitation analyses and morphological study. Four new species are described, including H.ephedrasp. nov., H.uwiiltilsp. nov., H.xericasp. nov., and H.zassp. nov. Females of H.encina Gertsch & Platnick, 1979 are also described for the first time. It is predicted that additional new species will ultimately be found in the mountains of central and northwestern Arizona, northern mainland Mexico, and the Mojave Desert of California.
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Affiliation(s)
- Rodrigo Monjaraz-Ruedas
- Department of Biology, San Diego State University, San Diego, California 92182–4614, USASan Diego State UniversitySan DiegoUnited States of America
| | | | - Marshal Hedin
- Department of Biology, San Diego State University, San Diego, California 92182–4614, USASan Diego State UniversitySan DiegoUnited States of America
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Keppel G, Sarnow U, Biffin E, Peters S, Fitzgerald D, Boutsalis E, Waycott M, Guerin GR. Population decline in a Pleistocene refugium: Stepwise, drought-related dieback of a South Australian eucalypt. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 876:162697. [PMID: 36898535 DOI: 10.1016/j.scitotenv.2023.162697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Refugia can facilitate the persistence of species under long-term environmental change, but it is not clear if Pleistocene refugia will remain functional as anthropogenic climate change progresses. Dieback in populations restricted to refugia therefore raises concerns about their long-term persistence. Using repeat field surveys, we investigate dieback in an isolated population of Eucalyptus macrorhyncha during two droughts and discuss prospects for its continued persistence in a Pleistocene refugium. We first confirm that the Clare Valley in South Australia has constituted a long-term refugium for the species, with the population being genetically highly distinct from other conspecific populations. However, the population lost >40 % of individuals and biomass through the droughts, with mortality being just below 20 % after the Millennium Drought (2000-2009) and almost 25 % after the Big Dry (2017-2019). The best predictors of mortality differed after each drought. While north-facing aspect of a sampling location was significant positive predictor after both droughts, biomass density and slope were significant negative predictors only after the Millennium Drought, and distance to the north-west corner of the population, which intercepts hot, dry winds, was a significant positive predictor after the Big Dry only. This suggests that more marginal sites with low biomass and sites located on flat plateaus were more vulnerable initially, but that heat-stress was an important driver of dieback during the Big Dry. Therefore, the causative drivers of dieback may change during population decline. Regeneration occurred predominantly on southern and eastern aspects, which would receive the least solar radiation. While this refugial population is experiencing severe decline, some gullies with lower solar radiation appear to support relatively healthy, regenerating stands of red stringybark, providing hope for persistence in small pockets. Monitoring and managing these pockets during future droughts will be essential to ensure the persistence of this isolated and genetically unique population.
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Affiliation(s)
- Gunnar Keppel
- UniSA STEM and Future Industries Institute, University of South Australia, GPO Box 2471, SA 5001 Adelaide, Australia; AMAP, Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France.
| | - Udo Sarnow
- UniSA STEM and Future Industries Institute, University of South Australia, GPO Box 2471, SA 5001 Adelaide, Australia
| | - Ed Biffin
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Department for Environment and Water, Adelaide, Australia.
| | - Stefan Peters
- UniSA STEM and Future Industries Institute, University of South Australia, GPO Box 2471, SA 5001 Adelaide, Australia.
| | - Donna Fitzgerald
- UniSA STEM and Future Industries Institute, University of South Australia, GPO Box 2471, SA 5001 Adelaide, Australia.
| | - Evan Boutsalis
- UniSA STEM and Future Industries Institute, University of South Australia, GPO Box 2471, SA 5001 Adelaide, Australia.
| | - Michelle Waycott
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Department for Environment and Water, Adelaide, Australia.
| | - Greg R Guerin
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia.
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Stiller J, Wilson NG, Rouse GW. Range-wide population genomics of common seadragons shows secondary contact over a former barrier and insights on illegal capture. BMC Biol 2023; 21:129. [PMID: 37248474 DOI: 10.1186/s12915-023-01628-9] [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: 01/26/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND Common seadragons (Phyllopteryx taeniolatus, Syngnathidae) are an emblem of the diverse endemic fauna of Australia's southern rocky reefs, the newly recognized "Great Southern Reef." A lack of assessments spanning this global biodiversity hotspot in its entirety is currently hampering an understanding of the factors that have contributed to its diversity. The common seadragon has a wide range across Australia's entire temperate south and includes a geogenetic break over a former land bridge, which has called its status as a single species into question. As a popular aquarium display that sells for high prices, common seadragons are also vulnerable to illegal capture. RESULTS Here, we provide range-wide nuclear sequences (986 variable Ultraconserved Elements) for 198 individuals and mitochondrial genomes for 140 individuals to assess species status, identify genetic units and their diversity, and trace the source of two poached individuals. Using published data of the other two seadragon species, we found that lineages of common seadragons have diverged relatively recently (< 0.63 Ma). Within common seadragons, we found pronounced genetic structure, falling into three major groups in the western, central, and eastern parts of the range. While populations across the Bassian Isthmus were divergent, there is also evidence for secondary contact since the passage opened. We found a strong cline of genetic diversity from the range center tapering symmetrically towards the range peripheries. Based on their genetic similarities, the poached individuals were inferred to have originated from around Albany in southwestern Australia. CONCLUSIONS We conclude that common seadragons constitute a single species with strong geographic structure but coherence through gene flow. The low genetic diversity on the east and west coasts is concerning given that these areas are projected to face fast climate change. Our results suggest that in addition to their life history, geological events and demographic expansions have all played a role in shaping populations in the temperate south. These insights are an important step towards understanding the historical determinants of the diversity of species endemic to the Great Southern Reef.
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Affiliation(s)
- Josefin Stiller
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA.
- Centre for Biodiversity Genomics, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - Nerida G Wilson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA
- Research & Collections, Western Australian Museum, Perth, Western Australia, 6106, Australia
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA.
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Garrido-Benavent I, de Los Ríos A, Núñez-Zapata J, Ortiz-Álvarez R, Schultz M, Pérez-Ortega S. Ocean crossers: a tale of disjunctions and speciation in the dwarf-fruticose Lichina (lichenized Ascomycota). Mol Phylogenet Evol 2023:107829. [PMID: 37247701 DOI: 10.1016/j.ympev.2023.107829] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/24/2022] [Accepted: 05/26/2023] [Indexed: 05/31/2023]
Abstract
Lichens thrive in rocky coastal areas in temperate and cold regions of both hemispheres. Species of the genus Lichina, which form characteristic black fruiting thalli associated with cyanobacteria, often create distinguishable bands in the intertidal and supralittoral zones. The present study uses a comprehensive specimen dataset and four gene loci to (1) delineate and discuss species boundaries in this genus, (2) assess evolutionary relationships among species, and (3) infer the most likely causes of their current geographic distribution in the Northern and Southern hemispheres. A dated phylogeny describes the time frame in which extant disjunctions of species and populations were established. The results showed that the genus is integrated by four species, with Lichina pygmaea, L. confinis and the newly described L. canariensis from rocky seashores in the Canary Islands, occurring in the Northern Hemisphere, whereas L. intermedia is restricted to the Southern Hemisphere. Lichina intermedia hosted a much higher intraspecific genetic diversity than the other species, with subclades interpreted as species-level lineages by the different species delimitation approaches. However, a conservative taxonomic approach was adopted. This species showed a striking disjunct distribution between Australasia and southern South America. The timing for the observed interspecific and intraspecific divergences and population disjunctions postdated continental plate movements, suggesting that long-distance dispersal across body waters in the two hemispheres played a major role in shaping the current species distributions. Such ocean crossings were, as in L. canariensis, followed by speciation. New substitution rates for the nrITS of the genus Lichina were inferred using a tree spanning the major Ascomycota lineages calibrated using fossils. In conclusion, this work lays the foundation for a better understanding of the evolution through time and space of maritime lichens.
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Affiliation(s)
- Isaac Garrido-Benavent
- Departament de Botànica i Geologia, Facultat de Ciències Biològiques, Universitat de València, C/ Doctor Moliner 50, E-46100-Burjassot, València, Spain; Department of Mycology, Real Jardín Botánico (CSIC), Plaza Murillo 2, E-28014 Madrid, Spain.
| | - Asunción de Los Ríos
- Department of Biogeochemistry and Microbial Ecology, National Museum of Natural Sciences (MNCN-CSIC), Serrano 115 dpdo, E-28045 Madrid, Spain.
| | - Jano Núñez-Zapata
- Department of Mycology, Real Jardín Botánico (CSIC), Plaza Murillo 2, E-28014 Madrid, Spain.
| | - Rüdiger Ortiz-Álvarez
- Department of International Science, Spanish Federation of Science and Technology (FECYT), C/ Pintor Murillo 15, E-28100 Alcobendas, Madrid, Spain.
| | - Matthias Schultz
- Herbarium Hamburgense, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststrasse 18, D-22609 Hamburg, Germany.
| | - Sergio Pérez-Ortega
- Department of Mycology, Real Jardín Botánico (CSIC), Plaza Murillo 2, E-28014 Madrid, Spain.
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Martins AB, Valença-Montenegro MM, Lima MGM, Lynch JW, Svoboda WK, Silva-Júnior JDSE, Röhe F, Boubli JP, Fiore AD. A New Assessment of Robust Capuchin Monkey ( Sapajus) Evolutionary History Using Genome-Wide SNP Marker Data and a Bayesian Approach to Species Delimitation. Genes (Basel) 2023; 14:genes14050970. [PMID: 37239330 DOI: 10.3390/genes14050970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 05/28/2023] Open
Abstract
Robust capuchin monkeys, Sapajus genus, are among the most phenotypically diverse and widespread groups of primates in South America, with one of the most confusing and often shifting taxonomies. We used a ddRADseq approach to generate genome-wide SNP markers for 171 individuals from all putative extant species of Sapajus to access their evolutionary history. Using maximum likelihood, multispecies coalescent phylogenetic inference, and a Bayes Factor method to test for alternative hypotheses of species delimitation, we inferred the phylogenetic history of the Sapajus radiation, evaluating the number of discrete species supported. Our results support the recognition of three species from the Atlantic Forest south of the São Francisco River, with these species being the first splits in the robust capuchin radiation. Our results were congruent in recovering the Pantanal and Amazonian Sapajus as structured into three monophyletic clades, though new morphological assessments are necessary, as the Amazonian clades do not agree with previous morphology-based taxonomic distributions. Phylogenetic reconstructions for Sapajus occurring in the Cerrado, Caatinga, and northeastern Atlantic Forest were less congruent with morphology-based phylogenetic reconstructions, as the bearded capuchin was recovered as a paraphyletic clade, with samples from the Caatinga biome being either a monophyletic clade or nested with the blond capuchin monkey.
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Affiliation(s)
- Amely Branquinho Martins
- Centro Nacional de Pesquisa e Conservação de Primatas Brasileiros, Instituto Chico Mendes de Conservação da Biodiversidade, Cabedelo 58310-000, PB, Brazil
- Primate Molecular Ecology and Evolution Laboratory, Department of Anthropology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Mônica Mafra Valença-Montenegro
- Centro Nacional de Pesquisa e Conservação de Primatas Brasileiros, Instituto Chico Mendes de Conservação da Biodiversidade, Cabedelo 58310-000, PB, Brazil
| | - Marcela Guimarães Moreira Lima
- Laboratório de Biogeografia da Conservação e Macroecologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66077-530, PA, Brazil
| | - Jessica W Lynch
- Institute for Society and Genetics, Department of Anthropology, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - Walfrido Kühl Svoboda
- Instituto Latino-Americano de Ciências da Vida e da Natureza, Centro Interdisciplinar de Ciências da Vida, Universidade Federal da Integração Latino-Americana, Foz do Iguaçu 85870-650, PR, Brazil
| | - José de Sousa E Silva-Júnior
- Museu Paraense Emílio Goeldi, Ministério da Ciência, Tecnologia, Inovações e Comunicações, Coordenação de Zoologia, Campus de Pesquisa, Setor de Mastozoologia, Belém 66077-830, PA, Brazil
| | - Fábio Röhe
- Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas, Manaus 69067-005, AM, Brazil
| | - Jean Philippe Boubli
- School of Science, Engineering and the Environment, University of Salford, Salford M5 4WT, UK
| | - Anthony Di Fiore
- Primate Molecular Ecology and Evolution Laboratory, Department of Anthropology, The University of Texas at Austin, Austin, TX 78712, USA
- Tiputini Biodiversity Station, Universidad San Francisco de Quito, Quito 170901, Ecuador
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Li YC, Gao ZL, Liu KJ, Tian JY, Yang BY, Rahman ZU, Yang LQ, Zhang SH, Li CT, Achilli A, Semino O, Torroni A, Kong QP. Mitogenome evidence shows two radiation events and dispersals of matrilineal ancestry from northern coastal China to the Americas and Japan. Cell Rep 2023:112413. [PMID: 37164007 DOI: 10.1016/j.celrep.2023.112413] [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: 07/28/2022] [Revised: 01/05/2023] [Accepted: 04/04/2023] [Indexed: 05/12/2023] Open
Abstract
Although it is widely recognized that the ancestors of Native Americans (NAs) primarily came from Siberia, the link between mitochondrial DNA (mtDNA) lineage D4h3a (typical of NAs) and D4h3b (found so far only in East China and Thailand) raises the possibility that the ancestral sources for early NAs were more variegated than hypothesized. Here, we analyze 216 contemporary (including 106 newly sequenced) D4h mitogenomes and 39 previously reported ancient D4h data. The results reveal two radiation events of D4h in northern coastal China, one during the Last Glacial Maximum and the other within the last deglaciation, which facilitated the dispersals of D4h sub-branches to different areas including the Americas and the Japanese archipelago. The coastal distributions of the NA (D4h3a) and Japanese lineages (D4h1a and D4h2), in combination with the Paleolithic archaeological similarities among Northern China, the Americas, and Japan, lend support to the coastal dispersal scenario of early NAs.
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Affiliation(s)
- Yu-Chun Li
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Zong-Liang Gao
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Kai-Jun Liu
- Chengdu 23Mofang Biotechnology Co., Ltd., Tianfu Software Park, Chengdu, Sichuan 610042, China
| | - Jiao-Yang Tian
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Bin-Yu Yang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Zia Ur Rahman
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Li-Qin Yang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Su-Hua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China
| | - Cheng-Tao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Ornella Semino
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China.
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Yang J, Skaro M, Chen J, Zhan D, Lyu L, Gay S, Kandeil A, Ali MA, Kayali G, Stoianova K, Ji P, Alabady M, Bahl J, Liu L, Arnold J. The species coalescent indicates possible bat and pangolin origins of the COVID-19 pandemic. Sci Rep 2023; 13:5571. [PMID: 37019985 PMCID: PMC10074375 DOI: 10.1038/s41598-023-32622-4] [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: 09/24/2022] [Accepted: 03/30/2023] [Indexed: 04/07/2023] Open
Abstract
A consensus species tree is reconstructed from 11 gene trees for human, bat, and pangolin beta coronaviruses from samples taken early in the pandemic (prior to April 1, 2020). Using coalescent theory, the shallow (short branches relative to the hosts) consensus species tree provides evidence of recent gene flow events between bat and pangolin beta coronaviruses predating the zoonotic transfer to humans. The consensus species tree was also used to reconstruct the ancestral sequence of human SARS-CoV-2, which was 2 nucleotides different from the Wuhan sequence. The time to most recent common ancestor was estimated to be Dec 8, 2019 with a bat origin. Some human, bat, and pangolin coronavirus lineages found in China are phylogenetically distinct, a rare example of a class II phylogeography pattern (Avise et al. in Ann Rev Eco Syst 18:489-422, 1987). The consensus species tree is a product of evolutionary factors, providing evidence of repeated zoonotic transfers between bat and pangolin as a reservoir for future zoonotic transfers to humans.
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Affiliation(s)
- Jialin Yang
- Statistics Department, University of Georgia, Athens, GA, USA
| | - Michael Skaro
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Jiani Chen
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Duna Zhan
- Statistics Department, University of Georgia, Athens, GA, USA
| | - Leke Lyu
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Skylar Gay
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- University of Texas School of Public Health, Houston, TX, USA
| | - Ahmed Kandeil
- National Research Centre, Cairo, Egypt
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Ghazi Kayali
- Human-Link DMCC, Dubai, UAE
- University of Texas School of Public Health, Houston, TX, USA
| | - Kateryna Stoianova
- Georgia Genomics and Bioinformatics Center, University of Georgia, Athens, GA, USA
| | - Pensheng Ji
- Statistics Department, University of Georgia, Athens, GA, USA
| | - Magdy Alabady
- Georgia Genomics and Bioinformatics Center, University of Georgia, Athens, GA, USA
- Plant Biology Department, University of Georgia, Athens, GA, USA
| | - Justin Bahl
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA, USA
| | - Liang Liu
- Statistics Department, University of Georgia, Athens, GA, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Jonathan Arnold
- Genetics Department, University of Georgia, Athens, GA, USA.
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Sil M, Roy A, Bhat HNP, Palden T, Karanth KP, Aravind NA. Role of paleoclimatic and paleohydrological processes in lineage divergence in freshwater organisms: A snippet from lentic genus Pila. Mol Phylogenet Evol 2023; 181:107723. [PMID: 36720420 DOI: 10.1016/j.ympev.2023.107723] [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: 11/18/2021] [Revised: 11/09/2022] [Accepted: 01/24/2023] [Indexed: 01/31/2023]
Abstract
The Indian subcontinent is extremely diverse in terms of its flora and fauna. However, only a handful of studies have aimed to understand the diversity of freshwater invertebrates using multiple lines of evidence in recent times. Here we aimed to estimate the cryptic diversity of two widespread freshwater snail species within the genus Pila (Röding, 1798) and uncover the processes behind lineage diversification in these species. We sequenced mitochondrial and nuclear markers from a comprehensive sampling of specimens from different river basins in India. We implemented an integrative taxonomy approach to delimit the lineages in these groups, employing phylogenetic, geometric morphometric and niche modelling-based methods. Then, we investigated the drivers of lineage divergence in these species using population genetic tools in conjunction with divergence time estimation. We found that both species consist of several genetically and ecologically distinct lineages. The genetic data showed that several of these lineages are restricted to a single or a few river basins. The divergence time estimation analyses indicated that the time frame of divergence within the species coincided with paleohydrological and paleoclimatic events in the Miocene. The diversification was primarily driven by allopatric isolation into different river basins. To conclude, the study sheds light on the complex interaction between the habitat preference of the species and the environment in shaping the diversification patterns in this group.
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Affiliation(s)
- Maitreya Sil
- Suri Sehgal Centre for Biodiversity and Conservation, Ashoka Trust for Research in Ecology and the Environment (ATREE), Royal Enclave, Srirampura, Jakkur PO, Bangalore 560064, India; National Institute for Science Education and Research, Bhubaneswar 752050, India.
| | - Abhisikta Roy
- Suri Sehgal Centre for Biodiversity and Conservation, Ashoka Trust for Research in Ecology and the Environment (ATREE), Royal Enclave, Srirampura, Jakkur PO, Bangalore 560064, India
| | - H N Poorna Bhat
- Suri Sehgal Centre for Biodiversity and Conservation, Ashoka Trust for Research in Ecology and the Environment (ATREE), Royal Enclave, Srirampura, Jakkur PO, Bangalore 560064, India
| | - Tenzin Palden
- Centre for Ecological Sciences, Indian Institute of Science, Malleshwaram, Bangalore 560012, India
| | - K Praveen Karanth
- Centre for Ecological Sciences, Indian Institute of Science, Malleshwaram, Bangalore 560012, India
| | - N A Aravind
- Suri Sehgal Centre for Biodiversity and Conservation, Ashoka Trust for Research in Ecology and the Environment (ATREE), Royal Enclave, Srirampura, Jakkur PO, Bangalore 560064, India; Yenepoya Research Centre, Yenepoya University, Derlakatte, Mangalore, India.
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Liu Y, Pu Y, Chen S, Wang X, Murphy RW, Wang X, Liao R, Tang K, Yue B, Liu S. Revalidation and expanded description of Mustela aistoodonnivalis (Mustelidae: Carnivora) based on a multigene phylogeny and morphology. Ecol Evol 2023; 13:e9944. [PMID: 37082328 PMCID: PMC10111237 DOI: 10.1002/ece3.9944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 03/02/2023] [Accepted: 03/13/2023] [Indexed: 04/22/2023] Open
Abstract
The lacked-teeth pygmy weasel, Mustela aistoodonnivalis Wu & Kao, 1991, was originally described as being from Taibai Mountain and Zhashui county, Shaanxi, China. Subsequently, it was considered a subspecies or synonym of Mustela nivalis. In a faunal survey of northwestern Sichuan, eight specimens of M. aistoodonnivalis were collected. A molecular phylogenetic analysis of one mitochondrial and six nuclear genes clustered the specimens as a distinct clade and not with M. nivalis. Morphologically, the lack of the second lower molar differentiated them from M. nivalis, and genetic distances were typical of discrete species. These analyses confirmed that M. aistoodonnivalis is an independent species in the genus Mustela.
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Affiliation(s)
- Yingxun Liu
- College of Life SciencesSichuan UniversityChengduSichuanChina
| | - Yingting Pu
- College of Life SciencesSichuan Normal UniversityChengduSichuanChina
| | - Shunde Chen
- College of Life SciencesSichuan Normal UniversityChengduSichuanChina
| | - Xuming Wang
- Sichuan Academy of ForestryChengduSichuanChina
| | | | - Xin Wang
- Sichuan Academy of ForestryChengduSichuanChina
| | - Rui Liao
- Sichuan Academy of ForestryChengduSichuanChina
| | - Keyi Tang
- College of Life SciencesSichuan Normal UniversityChengduSichuanChina
| | - Bisong Yue
- College of Life SciencesSichuan UniversityChengduSichuanChina
| | - Shaoying Liu
- Sichuan Academy of ForestryChengduSichuanChina
- Ecological Restoration and Conservation for Forest and Wetland Key Laboratory of Sichuan ProvinceSichuan Academy of ForestryChengduSichuanChina
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Yan Z, Ogilvie HA, Nakhleh L. Comparing inference under the multispecies coalescent with and without recombination. Mol Phylogenet Evol 2023; 181:107724. [PMID: 36720421 DOI: 10.1016/j.ympev.2023.107724] [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: 08/28/2022] [Revised: 01/17/2023] [Accepted: 01/24/2023] [Indexed: 01/29/2023]
Abstract
Accurate inference of population parameters plays a pivotal role in unravelling evolutionary histories. While recombination has been universally accepted as a fundamental process in the evolution of sexually reproducing organisms, it remains challenging to model it exactly. Thus, existing coalescent-based approaches make different assumptions or approximations to facilitate phylogenetic inference, which can potentially bring about biases in estimates of evolutionary parameters when recombination is present. In this article, we evaluate the performance of population parameter estimation using three methods-StarBEAST2, SNAPP, and diCal2-that represent three different types of inference. We performed whole-genome simulations in which recombination rates, mutation rates, and levels of incomplete lineage sorting were varied. We show that StarBEAST2 using short or medium-sized loci is robust to realistic rates of recombination, which is in agreement with previous studies. SNAPP, as expected, is generally unaffected by recombination events. Most surprisingly, diCal2, a method that is designed to explicitly account for recombination, performs considerably worse than other methods under comparison.
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Affiliation(s)
- Zhi Yan
- Department of Computer Science, Rice University, 6100 Main Street, Houston 77005, TX, USA.
| | - Huw A Ogilvie
- Department of Computer Science, Rice University, 6100 Main Street, Houston 77005, TX, USA.
| | - Luay Nakhleh
- Department of Computer Science, Rice University, 6100 Main Street, Houston 77005, TX, USA.
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Boo GH, Bottalico A, Le Gall L, Yoon HS. Genetic Diversity and Phylogeography of a Turf-Forming Cosmopolitan Marine Alga, Gelidium crinale (Gelidiales, Rhodo-Phyta). Int J Mol Sci 2023; 24:ijms24065263. [PMID: 36982334 PMCID: PMC10049384 DOI: 10.3390/ijms24065263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Cosmopolitan species are rare in red algae, which have a low-dispersal capacity unless they are dispersed by human-mediated introductions. Gelidium crinale, a turf-forming red alga, has a widespread distribution in tropical and temperate waters. To decipher the genetic diversity and phylogeography of G. crinale, we analyzed mitochondrial COI-5P and plastid rbcL sequences from collections in the Atlantic, Indian, and Pacific Oceans. Phylogenies of both markers statistically supported the monophyly of G. crinale, with a close relationship to G. americanum and G. calidum from the Western Atlantic. Based on the molecular analysis from these materials, Pterocladia heteroplatos from India is here merged with G. crinale. Phylogeny and TCS networks of COI-5P haplotypes revealed a geographic structure of five groups: (i) Atlantic-Mediterranean, (ii) Ionian, (iii) Asian, (iv) Adriatic-Ionian, and (v) Australasia-India-Tanzania-Easter Island. The most common ancestor of G. crinale likely diverged during the Pleistocene. The Bayesian Skyline Plots suggested the pre-LGM population expansion. Based on geographical structure, lineage-specific private haplotypes, the absence of shared haplotypes between lineages, and AMOVA, we propose that the cosmopolitan distribution of G. crinale has been shaped by Pleistocene relicts. The survival of the turf species under environmental stresses is briefly discussed.
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Affiliation(s)
- Ga Hun Boo
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Antonella Bottalico
- Department of Biosciences, Biotechnologies and Environment, University of Bari “A. Moro”, Via E. Orabona 4, 70125 Bari, Italy
| | - Line Le Gall
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, 75005 Paris, France
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Correspondence:
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Allman ES, Banos H, Rhodes JA. Testing Multispecies Coalescent Simulators Using Summary Statistics. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:1613-1618. [PMID: 35617176 PMCID: PMC10183998 DOI: 10.1109/tcbb.2022.3177956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
As genomic-scale datasets motivate research on species tree inference, simulators of the multispecies coalescent (MSC) process have become essential for the testing and evaluation of new inference methods. However, the simulators themselves must be tested to ensure that they give valid samples. This work develops methods for checking whether a collection of gene trees is in accord with the MSC model on a given species tree. When applied to well-known simulators, we find that several give flawed samples. The tests presented are capable of validating both topological and metric properties of gene tree samples, and are implemented in a freely available R package MSCsimtester so that developers and users may easily apply them.
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50
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Contrasting patterns of population structure of Bulwer's petrel (Bulweria bulwerii) between oceans revealed by statistical phylogeography. Sci Rep 2023; 13:1939. [PMID: 36732530 PMCID: PMC9895040 DOI: 10.1038/s41598-023-28452-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 01/18/2023] [Indexed: 02/04/2023] Open
Abstract
The patterns of population divergence of mid-latitude marine birds are impacted by only a few biogeographic barriers to dispersal and the effect of intrinsic factors, such as fidelity to natal colonies or wintering grounds, may become more conspicuous. Here we describe, for the first time, the phylogeographic patterns and historical demography of Bulwer's petrel Bulweria bulwerii and provide new insights regarding the drivers of species diversification in the marine environment. We sampled Bulwer's petrels from the main breeding colonies and used a statistical phylogeography approach based on surveying nuclear and mitochondrial loci (~ 9100 bp) to study its mechanisms of global diversification. We uncovered three highly differentiated groups including the Western Pacific, the Central Pacific and the Atlantic. The older divergence occurred within the Pacific Ocean, ca. 850,000 ya, and since then the W Pacific group has been evolving in isolation. Conversely, divergence between the Central Pacific and Atlantic populations occurred within the last 200,000 years. While the Isthmus of Panama is important in restricting gene flow between oceans in Bulwer's petrels, the deepest phylogeographic break is within the Pacific Ocean, where oceanographic barriers are key in driving and maintaining the remarkable structure found in this highly mobile seabird. This is in contrast with the Atlantic, where no structure was detected. Further data will provide insights regarding the extent of lineage divergence of Bulwer's petrels in the Western Pacific.
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