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Du H, Liu Z, Lu SY, Jiang L, Zhou L, Liu JF. Genomic evidence for human-mediated introgressive hybridization and selection in the developed breed. BMC Genomics 2024; 25:331. [PMID: 38565992 PMCID: PMC10986048 DOI: 10.1186/s12864-024-10259-5] [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: 09/26/2023] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND The pig (Sus Scrofa) is one of the oldest domesticated livestock species that has undergone extensive improvement through modern breeding. European breeds have advantages in lean meat development and highly-productive body type, whereas Asian breeds possess extraordinary fat deposition and reproductive performance. Consequently, Eurasian breeds have been extensively used to develop modern commercial breeds for fast-growing and high prolificacy. However, limited by the sequencing technology, the genome architecture of some nascent developed breeds and the human-mediated impact on their genomes are still unknown. RESULTS Through whole-genome analysis of 178 individuals from an Asian locally developed pig breed, Beijing Black pig, and its two ancestors from two different continents, we found the pervasive inconsistent gene trees and species trees across the genome of Beijing Black pig, which suggests its introgressive hybrid origin. Interestingly, we discovered that this developed breed has more genetic relationships with European pigs and an unexpected introgression from Asian pigs to this breed, which indicated that human-mediated introgression could form the porcine genome architecture in a completely different type compared to native introgression. We identified 554 genomic regions occupied 63.30 Mb with signals of introgression from the Asian ancestry to Beijing Black pig, and the genes in these regions enriched in pathways associated with meat quality, fertility, and disease-resistant. Additionally, a proportion of 7.77% of genomic regions were recognized as regions that have been under selection. Moreover, combined with the results of a genome-wide association study for meat quality traits in the 1537 Beijing Black pig population, two important candidate genes related to meat quality traits were identified. DNAJC6 is related to intramuscular fat content and fat deposition, and RUFY4 is related to meat pH and tenderness. CONCLUSIONS Our research provides insight for analyzing the origins of nascent developed breeds and genome-wide selection remaining in the developed breeds mediated by humans during modern breeding.
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Affiliation(s)
- Heng Du
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China
| | - Zhen Liu
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China
| | - Shi-Yu Lu
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China
| | - Li Jiang
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China
| | - Lei Zhou
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China.
| | - Jian-Feng Liu
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China.
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2
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Mônico PI, Soto-Centeno JA. Phylogenetic, morphological and niche differentiation unveil new species limits for the big brown bat ( Eptesicus fuscus). ROYAL SOCIETY OPEN SCIENCE 2024; 11:231384. [PMID: 38328571 PMCID: PMC10846953 DOI: 10.1098/rsos.231384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024]
Abstract
Phylogeographic accounts of mammals across fragmented landscapes show high levels of genetic, morphological and ecological variation. The big brown bat (Eptesicus fuscus) widely spans mainland landmasses from Canada to Ecuador and Colombia, and the insular Caribbean through The Bahamas and Greater and Lesser Antilles. Given the distribution of E. fuscus, we hypothesized that insular lineages could represent a different species aided by isolation. We assessed species limits by capitalizing on available mitochondrial and genomic data. Novel morphological and spatial datasets were produced to examine limits phenotypically and whether ecological niches could be associated with differences between groups. Phylogenetics strongly supported the Caribbean as unique compared to the mainland. Genomic data indicated high levels of genetic structure within the Caribbean and no detectable admixture of the Caribbean with continental lineages. Similarly, the Caribbean group shows high phenotypic disparity, and niche models revealed differences in habitat suitability between groups, concordant with the phylogenetic results. This study uncovered signals of divergence supporting the Caribbean clade of E. fuscus as unique through an integrative framework. We endorse re-evaluating the taxonomic status of Caribbean big brown bats as Eptesicus dutertreus. This recognition can help promote local conservation plans for insular lineages of big brown bats.
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Affiliation(s)
- Pedro Ivo Mônico
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ 07102, USA
| | - J. Angel Soto-Centeno
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ 07102, USA
- Department of Mammalogy, American Museum of Natural History, New York, NY 10024, USA
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3
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Ciccheto JRM, Razzolini EL, de Buron I, Boeger WA. Position of Polyclithrum within Gyrodactylidae (Monogenoidea): incongruences between morphological and molecular phylogenies. Syst Parasitol 2023; 100:633-645. [PMID: 37759094 DOI: 10.1007/s11230-023-10113-4] [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: 06/28/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023]
Abstract
This study aimed to enhance our understanding in monogenoid evolution by using morphological and molecular data to determine kinship relationships between species and changes in morphological structures over time. We focused on variations in characteristics among the organisms of the family Gyrodactylidae, concentrating on the phylogenetic position of Polyclithrum with other genera in the family. We collected specimens of Polyclithrum from the striped mullet, Mugil cephalus and Swingleus, and Fundulotrema specimens from mummichog Fundulus heteroclitus in estuarine systems of South Carolina, United States. In addition, we analyzed them and other genera (including e.g., Mormyrogyrodactylus, Gyrodactyloides, and Macrogyrodactylus) using both morphological and molecular (18S rDNA) approaches. We performed phylogenetic trees based on Maximum Parsymony, Maximum Likelihood and Bayesian Inference, and constructed a character morphological matrix by Parsimony Reconstruction of Ancestral Character States method. Our results suggest a homoplastic origin with evolutionary convergences in characters, revealing that there is inconsistency between our data and previously published works based solely on morphological structures of the group. The homoplasy scenario found in Gyrodactylidae can be a result of the limited set of putative homologous morphological features. However, differences between the phylogenies based on morphology and those based on molecular data may arise from both databases. While morphology remains essential in understanding the evolution of this group, molecular data, otherwise, provide a less biased source of information for constructing phylogenetic hypotheses. Combining these data facilitates a better comprehension of the homologous status of morphological features and to understand Gyrodactylidae evolutionary history.
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Affiliation(s)
- Juliana Rosa Matias Ciccheto
- Graduate Program in Ecology and Conservation, Department of Zoology, Biological Interactions, Federal University of Paraná, P.O. Box 19020, Curitiba, PR, 81531-890, Brazil.
| | - Emanuel Luis Razzolini
- Graduate Program in Bioprocess Engineering and Biotechnology, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, PR, Brazil
| | - Isaure de Buron
- Department of Biology, College of Charleston, Charleston, SC, 29424, USA
| | - Walter A Boeger
- Graduate Program in Ecology and Conservation, Department of Zoology, Biological Interactions, Federal University of Paraná, P.O. Box 19020, Curitiba, PR, 81531-890, Brazil
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4
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Lvarez R, Budaeva N. How complex is the Naineris setosa species complex? First integrative study of a presumed cosmopolitan and invasive annelid (Sedentaria: Orbiniidae). Zootaxa 2023; 5375:349-378. [PMID: 38220815 DOI: 10.11646/zootaxa.5375.3.3] [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: 11/22/2023] [Indexed: 01/16/2024]
Abstract
We performed a comparative study of the specimens from the Naineris setosa complex from the Pacific and the Atlantic Oceans and re-described the syntype of N. setosa, including the selection of the lectotype. Molecular phylogenetic and species delimitation analyses based on two mitochondrial (COI and 16S) and one nuclear (28S) marker revealed the presence of three species. One clade with wide Amphi-Atlantic distribution was attributed as Naineris setosa s. str. The second Atlantic clade restricted to Southern and Southeastern Brazil was described as a new species, Naineris lanai sp. n. The third clade, reported from the Northwestern Pacific, was identified as a new species but was not formally described due to the presence of only juvenile-sized worms in the studied material. Detailed morphological descriptions of several diagnostic characters in the Naineris setosa complex are provided.
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Affiliation(s)
- Ricardo Lvarez
- Graduate program in Oceanic Coastal Systems (PGSISCO); Federal University of Paran; Pontal do Paran; Paran; Brazil.
| | - Nataliya Budaeva
- Department of Natural History; University Museum of Bergen; University of Bergen; Allgaten 41; 5007 Bergen; Norway.
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5
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Aardema ML, Schmidt KL, Amato G. Patterns of cytonuclear discordance and divergence between subspecies of the scarlet macaw (Ara macao) in Central America. Genetica 2023; 151:281-292. [PMID: 37612519 PMCID: PMC10654179 DOI: 10.1007/s10709-023-00193-x] [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: 05/15/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023]
Abstract
The scarlet macaw, Ara macao, is a neotropical parrot that contains two described subspecies with broadly discrete geographical distributions. One subspecies, A. m. macao, is found from South America north into southwestern Costa Rica, while the second subspecies, A. m. cyanoptera, is found from eastern Costa Rica north into central Mexico. Our previous research using mitochondrial data to examine phylogeographical divergence across the collective range of these two subspecies concluded that they represent distinct evolutionary entities, with minimal contemporary hybridization between them. Here we further examine phylogenetic relationships and patterns of genetic variation between these two subspecies using a dataset of genetic markers derived from their nuclear genomes. Our analyses show clear nuclear divergence between A. m. macao and A. m. cyanoptera in Central America. Collectively however, samples from this region appear genetically more similar to one another than they do to the examined South American (Brazilian) A. m. macao sample. This observation contradicts our previous assessments based on mitochondrial DNA analyses that A. m. macao in Central and South America represent a single phylogeographical group that is evolutionarily distinct from Central American A. m. cyanoptera. Nonetheless, in agreement with our previous findings, ongoing genetic exchange between the two subspecies appears limited. Rather, our analyses indicate that incomplete lineage sorting is the best supported explanation for cytonuclear discordance within these parrots. High-altitude regions in Central America may act as a reproductive barrier, limiting contemporary hybridization between A. m. macao and A. m. cyanoptera. The phylogeographic complexities of scarlet macaw taxa in this region highlight the need for additional evolutionary examinations of these populations.
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Affiliation(s)
- Matthew L Aardema
- Department of Biology, Montclair State University, Montclair, NJ, 07043, USA.
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.
| | - Kari L Schmidt
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
| | - George Amato
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
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Gautney JR. A new approach to exploratory data analysis in hominin phylogenetic reconstruction. J Hum Evol 2023; 182:103412. [PMID: 37499423 DOI: 10.1016/j.jhevol.2023.103412] [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: 09/23/2022] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 07/29/2023]
Abstract
The phylogenetic relationships between fossil hominin taxa have been a contentious topic for decades. Recent discoveries of new taxa, rather than resolving the issue, have only further confused it. Compounding this problem are the limitations of some of the tools frequently used by paleoanthropologists to analyze these relationships. Most commonly, phylogenetic questions are investigated using analytical methods such as maximum parsimony and Bayesian analysis. While these are useful analytical tools, these tree-building methods can have limitations when investigating taxa that may have complex evolutionary histories. Exploratory data analysis can provide information about patterns in a dataset that are obscured by tree-based methods. These patterns include phylogenetic signal conflict, which is not depicted in tree-based methods. Signal conflict can have a number of sources, including methodological issues with character choice, taxonomic issues, homoplasy, and gene flow between taxa. In this study, an exploratory data analysis of fossil hominin morphological data is conducted using the tree-based analytical method neighbor-joining and the network-based analytical method neighbor-net with the goal of visualizing phylogenetic signal conflict within a hominin morphological data set. The data set is divided into cranial regions, and each cranial region is analyzed individually to investigate which regions of the skull contain the highest levels of signal conflict. Results of this analysis show that conflicting phylogenetic signals are present in the hominin fossil record during the relatively speciose period between 3 and 1 Ma, and they also indicate that levels of signal conflict vary by cranial region. Possible sources of these conflicting signals are then explored. Exploratory data analyses such as this can be a useful tool in generating phylogenetic hypotheses and in refining character choice. This study also highlights the value network-based approaches can bring to the hominin phylogenetic analysis toolkit.
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Affiliation(s)
- Joanna R Gautney
- Department of Sociology and Anthropology, Weber State University, 1299 Edvalson St., Ogden, UT, USA.
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7
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DeSalle R, Narechania A, Tessler M. Multiple Outgroups Can Cause Random Rooting in Phylogenomics. Mol Phylogenet Evol 2023; 184:107806. [PMID: 37172862 DOI: 10.1016/j.ympev.2023.107806] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 02/06/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
Outgroup selection has been a major challenge since the rise of phylogenetics, and it has remained so in the phylogenomic era. Our goal here is to use large phylogenomic animal datasets to examine the impact of outgroup selection on the final topology. The results of our analyses further solidify the fact that distant outgroups can cause random rooting, and that this holds for concatenated and coalescent-based methods. The results also indicate that the standard practice of using multiple outgroups often causes random rooting. Most researchers go out of their way to get multiple outgroups, as this has been standard practice for decades. Based on our findings, this practice should stop. Instead, our results suggest that a single (most closely) related relative should be selected as the outgroup, unless all outgroups are roughly equally closely related to the ingroup.
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Affiliation(s)
- Rob DeSalle
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA; Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Apurva Narechania
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Michael Tessler
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA; Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA; St. Francis College, Department of Biology, Brooklyn, NY 11201, USA
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8
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Ayala-Berdon J, Martínez Gómez M, Ponce AR, Beamonte-Barrientos R, Vázquez J, Rodriguez-Peña ON. Weather, ultrasonic, cranial and body traits predict insect diet hardness in a Central Mexican bat community. MAMMAL RES 2023. [DOI: 10.1007/s13364-023-00678-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
Abstract
AbstractInsectivorous bats exhibit food preferences for specific attributes in their prey. Hardness has been defined as an important prey attribute, and in some cases a limiting factor in foraging decisions for smaller compared to larger bat species. The goal of this study was to identify which factors influence the selection of prey hardness in a vespertilionid bat community. We investigated food consumed by bats by analyzing fecal samples obtained from eight bat species coexisting in a mountain ecosystem of central Mexico and correlate non-phylogenetically and phylogenetically prey hardness to weather, bat´s body, cranial and ultrasonic call structure variables. Results showed that diet of vespertilionid bats was mainly represented by Diptera, Neuroptera, Lepidoptera and Coleoptera consumption. The qualitative prey hardness index (From soft 1 to hard 5) ranked bats as: Myotis melanorhinus, Corynorhinus mexicanus, Myotis volans, Myotis californicus (< 3); Myotis velifer (< 4); Eptesicus fuscus, Idionycteris phyllotis and Myotis thysanodes (> 4.2). Prey hardness was positively correlated to minimum and mean temperatures, bat´s body weight, total and forearm lengths, cranial variables as: zygomatic breadth, mandibular length, height of the coronoid process, lower molar width, C-M3 superior and inferior rows length and upper molar width; and negatively to ultrasonic variables as total slope, call duration, low and high frequencies, band width and frequency maximum power. Considering phylogenies, prey hardness positively correlated to mandibular length, C-M3 inferior and superior rows lengths (p < 0.05). Our results showed that environmental, morphological and echolocation variables can be used as predictors of preferred insect prey in a community of vespertilionid bats.
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9
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Camacho MA, Cadar D, Horváth B, Merino-Viteri A, Murienne J. Revised phylogeny from complete mitochondrial genomes of phyllostomid bats resolves subfamilial classification. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Classically, molecular phylogenetic trees of Phyllostomidae have been inferred using a combination of a few mitochondrial and nuclear markers. However, there is still uncertainty in the relationships, especially among deep clades within the family. In this study, we provide newly sequenced complete mitochondrial genomes from 26 bat species, including genomes of 23 species reported here for the first time. By carefully analysing these genomes using maximum likelihood and Bayesian methods and different ingroup and outgroup samples, partition schemes and data types, we investigated the robustness and sensitivity of our phylogenetic results. The optimal topologies were those inferred from the complete data matrix of nucleotides, with complex and highly parameterized substitution models and partition schemes. Our results show a statistically robust picture of the evolutionary relationships between phyllostomid subfamilies and clarify hitherto uncertain relationships of Lonchorhininae and Macrotinae.
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Affiliation(s)
- M Alejandra Camacho
- Museo de Zoología (QCAZ), Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador , Quito, Pichincha , Ecuador
- Laboratoire Evolution et Diversité Biologique (UMR5174), CNRS, IRD, Université Paul Sabatier , Toulouse , France
| | - Dániel Cadar
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, BernhardNocht Institute for Tropical Medicine , Hamburg , Germany
| | - Balázs Horváth
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, BernhardNocht Institute for Tropical Medicine , Hamburg , Germany
| | - Andrés Merino-Viteri
- Museo de Zoología (QCAZ), Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador , Quito, Pichincha , Ecuador
- Laboratorio de Ecofisiología, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católicadel Ecuador , Quito, Pichincha , Ecuador
| | - Jérôme Murienne
- Laboratoire Evolution et Diversité Biologique (UMR5174), CNRS, IRD, Université Paul Sabatier , Toulouse , France
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10
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Beck RM, Voss RS, Jansa SA. Craniodental Morphology and Phylogeny of Marsupials. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2022. [DOI: 10.1206/0003-0090.457.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Robin M.D. Beck
- School of Science, Engineering and Environment University of Salford, U.K. School of Biological, Earth & Environmental Sciences University of New South Wales, Australia Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Robert S. Voss
- Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Sharon A. Jansa
- Bell Museum and Department of Ecology, Evolution, and Behavior University of Minnesota
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11
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Feng S, Bai M, Rivas-González I, Li C, Liu S, Tong Y, Yang H, Chen G, Xie D, Sears KE, Franco LM, Gaitan-Espitia JD, Nespolo RF, Johnson WE, Yang H, Brandies PA, Hogg CJ, Belov K, Renfree MB, Helgen KM, Boomsma JJ, Schierup MH, Zhang G. Incomplete lineage sorting and phenotypic evolution in marsupials. Cell 2022; 185:1646-1660.e18. [PMID: 35447073 PMCID: PMC9200472 DOI: 10.1016/j.cell.2022.03.034] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 12/22/2021] [Accepted: 03/21/2022] [Indexed: 12/19/2022]
Abstract
Incomplete lineage sorting (ILS) makes ancestral genetic polymorphisms persist during rapid speciation events, inducing incongruences between gene trees and species trees. ILS has complicated phylogenetic inference in many lineages, including hominids. However, we lack empirical evidence that ILS leads to incongruent phenotypic variation. Here, we performed phylogenomic analyses to show that the South American monito del monte is the sister lineage of all Australian marsupials, although over 31% of its genome is closer to the Diprotodontia than to other Australian groups due to ILS during ancient radiation. Pervasive conflicting phylogenetic signals across the whole genome are consistent with some of the morphological variation among extant marsupials. We detected hundreds of genes that experienced stochastic fixation during ILS, encoding the same amino acids in non-sister species. Using functional experiments, we confirm how ILS may have directly contributed to hemiplasy in morphological traits that were established during rapid marsupial speciation ca. 60 mya.
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Affiliation(s)
- Shaohong Feng
- BGI-Shenzhen, Shenzhen 518083, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Ming Bai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; School of Agriculture, Ningxia University, Yinchuan 750021, China; College of Plant Protection, Hebei Agricultural University, Baoding 071001, China
| | | | - Cai Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | | | - Yijie Tong
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei 071001, China; Hainan Yazhou Bay Seed Lab, Building 1, No. 7 Yiju Road, Yazhou District, Sanya, Hainan 572024, China
| | - Haidong Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Guangji Chen
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Duo Xie
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Lida M Franco
- Facultad de Ciencias Naturales y Matemáticas, Universidad de Ibagué, Carrera 22 Calle 67, Ibagué, Colombia
| | - Juan Diego Gaitan-Espitia
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Roberto F Nespolo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile; Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago 6513677, Chile; Millenium Institute for Integrative Biology (iBio), Santiago, Chile; Millennium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
| | - Warren E Johnson
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remont Road, Front Royal, VA 22630, USA; The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, 4210 Silver Hill Rd., Suitland, MD 20746-2863, USA; Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Parice A Brandies
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia; Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jacobus J Boomsma
- Section for Ecology and Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Guojie Zhang
- BGI-Shenzhen, Shenzhen 518083, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, 2100 Copenhagen, Denmark; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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12
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Gaunt MW, Pettersson JHO, Kuno G, Gaunt B, de Lamballerie X, Gould EA. Widespread Interspecific Phylogenetic Tree Incongruence Between Mosquito-Borne and Insect-Specific Flaviviruses at Hotspots Originally Identified in Zika Virus. Virus Evol 2022; 8:veac027. [PMID: 35591877 PMCID: PMC9113262 DOI: 10.1093/ve/veac027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 10/22/2021] [Accepted: 04/17/2022] [Indexed: 11/16/2022] Open
Abstract
Intraspecies (homologous) phylogenetic incongruence, or ‘tree conflict’ between different loci within the same genome of mosquito-borne flaviviruses (MBFV), was first identified in dengue virus (DENV) and subsequently in Japanese encephalitis virus (JEV), St Louis encephalitis virus, and Zika virus (ZIKV). Recently, the first evidence of phylogenetic incongruence between interspecific members of the MBFV was reported in ZIKV and its close relative, Spondweni virus. Uniquely, these hybrid proteomes were derived from four incongruent trees involving an Aedes-associated DENV node (1 tree) and three different Culex-associated flavivirus nodes (3 trees). This analysis has now been extended across a wider spectrum of viruses within the MBFV lineage targeting the breakpoints between phylogenetic incongruent loci originally identified in ZIKV. Interspecies phylogenetic incongruence at these breakpoints was identified in 10 of 50 viruses within the MBFV lineage, representing emergent Aedes and Culex-associated viruses including JEV, West Nile virus, yellow fever virus, and insect-specific viruses. Thus, interspecies phylogenetic incongruence is widespread amongst the flaviviruses and is robustly associated with the specific breakpoints that coincide with the interspecific phylogenetic incongruence previously identified, inferring they are ‘hotspots’. The incongruence amongst the emergent MBFV group was restricted to viruses within their respective associated epidemiological boundaries. This MBFV group was RY-coded at the third codon position (‘wobble codon’) to remove transition saturation. The resulting ‘wobble codon’ trees presented a single topology for the entire genome that lacked any robust evidence of phylogenetic incongruence between loci. Phylogenetic interspecific incongruence was therefore observed for exactly the same loci between amino acid and the RY-coded ‘wobble codon’ alignments and this incongruence represented either a major part, or the entire genomes. Maximum likelihood codon analysis revealed positive selection for the incongruent lineages. Positive selection could result in the same locus producing two opposing trees. These analyses for the clinically important MBFV suggest that robust interspecific phylogenetic incongruence resulted from amino acid selection. Convergent or parallel evolutions are evolutionary processes that would explain the observation, whilst interspecific recombination is unlikely.
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Affiliation(s)
- Michael W Gaunt
- London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - John H-O Pettersson
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, the University of Sydney, Sydney, New South Wales 2006, Australia
| | - Goro Kuno
- Formerly, Centers for Disease Control, Fort Collins, CO 80521, USA
| | - Bill Gaunt
- Aeon-sys, MBCS Kensington Road, Barnsley S75 2TU, UK
| | - Xavier de Lamballerie
- UMR “Unité des Virus Emergents”, Aix-Marseille Université-IRD 190-Inserm 1207-IHU Méditerranée Infection, Marseille, France
- APHM Public Hospitals of Marseille, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Ernest A Gould
- UMR “Unité des Virus Emergents”, Aix-Marseille Université-IRD 190-Inserm 1207-IHU Méditerranée Infection, Marseille, France
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13
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Baeza JA, Rodríguez ME, Ortega J. A genomic portrait of Sturnira parvidens: mitochondrial chromosome, repetitive elements, and microsatellite discovery. J Mammal 2021. [DOI: 10.1093/jmammal/gyab117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
The yellow-shouldered bat, Sturnira parvidens (Phyllostomidae), is an abundant and widespread species in southern North America and Mesoamerica. Despite its important ecological role, no genomic resources exist for this species. Using low-coverage short Illumina 150 bp pair-end reads sequencing, this study reports the mitochondrial chromosome and nuclear repetitive elements, including microsatellites, in S. parvidens. The mitochondrial genome of S. parvidens is 16,612 bp in length and is comprised of 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Repetitive elements constituted ~67% of the nuclear genome while ~33% of the genome represented single- or low-copy sequences. A moderate proportion of repetitive sequences (31% putative families) could not be assigned to known repeat element families. Considering only annotated repetitive elements, the most ubiquitous repetitive elements belonged to Class I-LINE and Satellite DNA, which were considerably more abundant than Class I-LTR elements and Class II-DNA transposons (TcMar-Mariner and hAT-Charlie). A total of 193 microsatellites were identified.
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Affiliation(s)
- J Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
- Smithsonian Marine Station at Fort Pierce, Fort Pierce, Florida, USA
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, Coquimbo, Chile
| | - Melissa E Rodríguez
- Programa de Conservación de Murciélagos de El Salvador (PCMES) de la Asociación Territorios Vivos El Salvador (ATVES), Calle las Acacias, Col. Vista Hermosa #120, San Salvador, El Salvador
| | - Jorge Ortega
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoologia, Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, Prolongacion de Carpio y Plan de Ayala s/n, Col. Sto. Tomas, CDMX, Mexico
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14
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Zhang G, Geng D, Guo Q, Liu W, Li S, Gao W, Wang Y, Zhang M, Wang Y, Bu Y, Niu H. Genomic landscape of mitochondrial DNA insertions in 23 bat genomes: characteristics, loci, phylogeny, and polymorphism. Integr Zool 2021; 17:890-903. [PMID: 34496458 DOI: 10.1111/1749-4877.12582] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The transfer of mitochondrial DNA to the nuclear genome gives rise to the nuclear DNA sequences of mitochondrial origin (NUMTs), considered as a driving force in genome evolution. In this study, NUMTs in 23 bat genomes were investigated and compared systematically. The results showed that NUMTs existed in 22 genomes except for Noctilio leporinus, suggesting that mitochondrial fragment insertion in the nuclear genome was a common event in bat genomes. However, remarkable variations in NUMTs number, cumulative length, and proportion in the nuclear genome were discovered across bat species. Further orthologous NUMT loci analysis of the Phyllostomidae family indicated that the NUMTs insertion events in bat genomes were homoplasy-free. The NUMTs were mainly inserted into the intergenic regions, particularly, co-localized with repetitive sequences (especially transposable elements). However, several NUMTs were inserted into genes, some of which were in the exon region of functional genes. One NUMT in the genome of Pteropus alecto surprisingly matched with cDNA of ATP8B3 that provided evidence of NUMTs with coding function. Phylogenic analysis on NUMTs originating from COXI and COXII loci highlighted 2 clusters of Yinpterochiroptera and Yangochiroptera for Chiroptera. Seven NUMTs from Rhinolophus ferrumequinum were amplified, and the sequencing results confirmed the reliability of the NUMT analysis. One of them was polymorphic for the presence or absence of the NUMT insertion, and each genotype of NUMT loci showed a distinct regional distribution pattern. The information obtained in this study provides novel insights into the NUMT organization and features in bat genomes and establishes a basis for further studying of the evolution of bat species.
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Affiliation(s)
- Guojun Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, China.,School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Deqi Geng
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Qiulin Guo
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Wei Liu
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Shufen Li
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Wujun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Yongfei Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Min Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Yilin Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Yanzhen Bu
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Hongxing Niu
- College of Life Sciences, Henan Normal University, Xinxiang, China
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15
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Velazco PM, Voss RS, Fleck DW, Simmons NB. Mammalian Diversity and Matses Ethnomammalogy in Amazonian Peru Part 4: Bats. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2021. [DOI: 10.1206/0003-0090.451.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Paúl M. Velazco
- Department of Biology, Arcadia University, Glenside, PA; Division of Vertebrate Zoology (Mammalogy), American Museum of Natural History
| | - Robert S. Voss
- Division of Vertebrate Zoology (Mammalogy), American Museum of Natural History
| | - David W. Fleck
- Division of Anthropology, American Museum of Natural History
| | - Nancy B. Simmons
- Division of Vertebrate Zoology (Mammalogy), American Museum of Natural History
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16
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Moreno JM, Jesus TF, Coelho MM, Sousa VC. Adaptation and convergence in circadian-related genes in Iberian freshwater fish. BMC Ecol Evol 2021; 21:38. [PMID: 33685402 PMCID: PMC7941933 DOI: 10.1186/s12862-021-01767-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 02/16/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The circadian clock is a biological timing system that improves the ability of organisms to deal with environmental fluctuations. At the molecular level it consists of a network of transcription-translation feedback loops, involving genes that activate (bmal and clock - positive loop) and repress expression (cryptochrome (cry) and period (per) - negative loop). This is regulated by daily alternations of light but can also be affected by temperature. Fish, as ectothermic, depend on the environmental temperature and thus are good models to study its integration within the circadian system. Here, we studied the molecular evolution of circadian genes in four Squalius freshwater fish species, distributed across Western Iberian rivers affected by two climatic types with different environmental conditions (e.g., light and temperature). S. carolitertii and S. pyrenaicus inhabit the colder northern region under Atlantic climate type, while S. torgalensis, S. aradensis and some populations of S. pyrenaicus inhabit the warmer southern region affected by summer droughts, under Mediterranean climate type. RESULTS We identified 16 circadian-core genes in the Squalius species using a comparative transcriptomics approach. We detected evidence of positive selection in 12 of these genes using methods based on dN/dS. Positive selection was mainly found in cry and per genes of the negative loop, with 55 putatively adaptive substitutions, 16 located on protein domains. Evidence for positive selection is predominant in southern populations affected by the Mediterranean climate type. By predicting protein features we found that changes at sites under positive selection can impact protein thermostability by changing their aliphatic index and isoelectric point. Additionally, in nine genes, the phylogenetic clustering of species that belong to different clades but inhabit southern basins with similar environmental conditions indicated evolutionary convergence. We found evidence for increased nonsynonymous substitution rate in convergent lineages, likely due to positive selection at 27 sites, mostly in cry genes. CONCLUSIONS Our results support that temperature may be a selective pressure driving the evolution of genes involved in the circadian system. By integrating sequence-based functional protein prediction with dN/dS-based methods to detect selection we uncovered adaptive convergence in the southern populations, probably related to their similar thermal conditions.
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Affiliation(s)
- João M Moreno
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Tiago F Jesus
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Maria M Coelho
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Vitor C Sousa
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.
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17
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Calahorra-Oliart A, Ospina-Garcés SM, León-Paniagua L. Cryptic species in Glossophaga soricina (Chiroptera: Phyllostomidae): do morphological data support molecular evidence? J Mammal 2021. [DOI: 10.1093/jmammal/gyaa116] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Abstract
Cryptic species, defined as those that are morphologically indistinguishable but phylogenetically distinct, are common in bats and correspond to the majority of newly described species. Such seems to be the case of Glossophaga soricina, a generalist, glossophagine bat that is broadly distributed throughout the Neotropics. Several studies have found high levels of molecular variation within G. soricina, suggesting that it could be a cryptic species complex. Here, we explore data derived from two-dimensional geometric morphometric analyses of cranial characters and their covariation with environmental variables, aiming to test the existence of more than one species grouped within it and to contribute to the knowledge of its variation and evolutionary history. Variation in shape and size of skull and mandible supports the two main mitochondrial lineages reported in previous studies, one corresponding to the east side of the Andes (subspecies G. s. soricina) and the other one corresponding to populations from Mesoamerica and the west side of the Andes, in turn composed of at least three monophyletic and morphologically differentiated taxa. Environmental variables correlate with shape variation and might be responsible for convergences in shape and size between the species with the smallest distributions. Based on the evidence we present in this work we elevate four subspecies to the taxonomic level of species. The correct names for the species of the analyzed complex are: G. soricina (Pallas 1766), G. mutica Merriam 1898, G. antillarum Rehn 1902, and G. valens Miller 1913.
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Affiliation(s)
- Adriana Calahorra-Oliart
- Museo de Zoología “Alfonso L. Herrera,” Facultad de Ciencias, Universidad Nacional Autónoma de México, México, D.F., Mexico
| | - Sandra M Ospina-Garcés
- Museo de Zoología “Alfonso L. Herrera,” Facultad de Ciencias, Universidad Nacional Autónoma de México, México, D.F., Mexico
| | - Livia León-Paniagua
- Museo de Zoología “Alfonso L. Herrera,” Facultad de Ciencias, Universidad Nacional Autónoma de México, México, D.F., Mexico
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18
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Basantes M, Tinoco N, Velazco PM, Hofmann MJ, Rodríguez-Posada ME, Camacho MA. Systematics and Taxonomy of Tonatia saurophila Koopman & Williams, 1951 (Chiroptera, Phyllostomidae). Zookeys 2020; 915:59-86. [PMID: 32148423 PMCID: PMC7052022 DOI: 10.3897/zookeys.915.46995] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/29/2019] [Indexed: 12/04/2022] Open
Abstract
The Stripe-headed Round-eared bat, Tonatiasaurophila, includes three subspecies: Tonatiasaurophilasaurophila (known only from subfossil records in Jamaica), Tonatiasaurophilabakeri (distributed from southeastern Mexico to northern Colombia, Venezuela west and north of the Cordillera de Mérida, and northwestern Ecuador), and Tonatiasaurophilamaresi (distributed in Venezuela east and south of the Cordillera de Mérida, the Guianas, Trinidad and Tobago, northeastern Brazil, and along the upper Amazon basin in Colombia, Ecuador, Peru, and Bolivia). The last two subspecies are an attractive example to test predictions about the historical role of the Andes in mammalian diversification. Based on morphological descriptions, morphometric analyses, and phylogenetic reconstruction using the mitochondrial gene Cyt-b and the nuclear exon RAG2, this study evaluates the intraspecific relationships within Tonatiasaurophila and the taxonomic status of the taxon. The three subspecies of T.saurophila are recognizable as full species: Tonatiabakeri, Tonatiamaresi, and Tonatiasaurophila. The latter is restricted to its type locality and possibly is extinct. Tonatiabakeri, in addition to being larger than T.maresi, is morphologically distinguishable by possessing an acute apex at the posterior edge of the skull, a well-developed clinoid process, and relatively robust mandibular condyles, and by lacking a diastema between the canine and the first lower premolar. The genetic distance between T.bakeri and T.maresi is 7.65%.
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Affiliation(s)
- Mateo Basantes
- Sección de Mastozoología, Museo de Zoología, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Pichincha, Ecuador Pontificia Universidad Católica del Ecuador Quito Ecuador
| | - Nicolás Tinoco
- Sección de Mastozoología, Museo de Zoología, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Pichincha, Ecuador Pontificia Universidad Católica del Ecuador Quito Ecuador
| | - Paúl M Velazco
- Department of Mammalogy, American Museum of Natural History, Central Park West at 79th St., New York, NY 10024, USA American Museum of Natural History New York United States of America.,Department of Biology, Arcadia University, 450 S. Easton Rd., Glenside, PA 19038, USA Arcadia University Glenside United States of America
| | - Melinda J Hofmann
- Sección de Mastozoología, Museo de Zoología, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Pichincha, Ecuador Pontificia Universidad Católica del Ecuador Quito Ecuador
| | - Miguel E Rodríguez-Posada
- Fundación Reserva Natural La Palmita, Centro de Investigación, Grupo de Investigaciones Territoriales para el Uso y Conservación de la Biodiversidad, Bogotá, Colombia Grupo de Investigaciones Territoriales para el Uso y Conservación de la Biodiversidad Bogotá Colombia
| | - M Alejandra Camacho
- Sección de Mastozoología, Museo de Zoología, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Pichincha, Ecuador Pontificia Universidad Católica del Ecuador Quito Ecuador
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19
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Insights into the assembly rules of a continent-wide multilayer network. Nat Ecol Evol 2019; 3:1525-1532. [PMID: 31611677 DOI: 10.1038/s41559-019-1002-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 09/12/2019] [Indexed: 11/08/2022]
Abstract
How are ecological systems assembled? Identifying common structural patterns within complex networks of interacting species has been a major challenge in ecology, but researchers have focused primarily on single interaction types aggregating in space or time. Here, we shed light on the assembly rules of a multilayer network formed by frugivory and nectarivory interactions between bats and plants in the Neotropics. By harnessing a conceptual framework known as the integrative hypothesis of specialization, our results suggest that phylogenetic constraints separate species into different layers and shape the network's modules. Then, the network shifts to a nested structure within its modules where interactions are mainly structured by geographic co-occurrence. Finally, organismal traits related to consuming fruits or nectar determine which bat species are central or peripheral to the network. Our results provide insights into how different processes contribute to the assemblage of ecological systems at different levels of organization, resulting in a compound network topology.
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20
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Solari S, Sotero-Caio CG, Baker RJ. Advances in systematics of bats: towards a consensus on species delimitation and classifications through integrative taxonomy. J Mammal 2019. [DOI: 10.1093/jmammal/gyy168] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Sergio Solari
- Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Cibele G Sotero-Caio
- Departamento de Genética, Universidade Federal de Pernambuco, Cidade Universitária, Recife, PE, Brazil
| | - Robert J Baker
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
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21
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Eyer PA, Hefetz A. Cytonuclear incongruences hamper species delimitation in the socially polymorphic desert ants of the Cataglyphis albicans group in Israel. J Evol Biol 2018; 31:1828-1842. [PMID: 30240036 DOI: 10.1111/jeb.13378] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 08/01/2018] [Accepted: 09/13/2018] [Indexed: 11/27/2022]
Abstract
Assessing whether behavioural, ecological or geographical factors trigger population divergence provides key insights into the biological processes driving speciation. Recent speciation in restricted geographic area without obvious ecological barriers prompts the question of the behavioural mechanisms underlying species divergence. In this context, we investigated phylogenetic relationships in the Cataglyphis albicans desert ant complex in Israel. We first determined accurate species delimitation using two mitochondrial and six nuclear genes, as well as 11 microsatellite markers to investigate cryptic species in this group, assessing reduction in gene flow between populations. We then investigated whether different species in this group exhibit distinct reproductive strategies, inferring social structure and queen-mating frequency in each species uncovered. Our findings highlight the presence of at least six distinct Cataglyphis albicans species in the restricted range of Israel; four of them co-occur in a 50 × 50 km area in North Negev, while two are endemic from there. However, our results reveal incongruences between nuclear and mitochondrial clustering, which complicate species identification and preclude the exclusive use of mtDNA to confidently delimit species in this group. Finally, we show that the different species of the C. albicans group in Israel exhibit quite similar reproductive strategies with most of them having colonies headed by a single queen mated with several males; colonies of one species were, however, headed by several queens. Overall, this weak variation across species thereby unlikely represents the main evolutionary force behind speciation of these sympatric species. We then discuss the potential evolutionary processes that underlie speciation in this group in the absence of clear geographical or ecological barriers.
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Affiliation(s)
- Pierre-André Eyer
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Abraham Hefetz
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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22
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Wu J, Jiao H, Simmons NB, Lu Q, Zhao H. Testing the sensory trade-off hypothesis in New World bats. Proc Biol Sci 2018; 285:rspb.2018.1523. [PMID: 30158315 DOI: 10.1098/rspb.2018.1523] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/04/2018] [Indexed: 01/03/2023] Open
Abstract
Detection of evolutionary shifts in sensory systems is challenging. By adopting a molecular approach, our earlier study proposed a sensory trade-off hypothesis between a loss of colour vision and an origin of high-duty-cycle (HDC) echolocation in Old World bats. Here, we test the hypothesis in New World bats, which include HDC echolocators that are distantly related to Old World HDC echolocators, as well as vampire bats, which have an infrared sensory system apparently unique among bats. Through sequencing the short-wavelength opsin gene (SWS1) in 16 species (29 individuals) of New World bats, we identified a novel SWS1 polymorphism in an HDC echolocator: one allele is pseudogenized but the other is intact, while both alleles are either intact or pseudogenized in other individuals. Strikingly, both alleles were found to be pseudogenized in all three vampire bats. Since pseudogenization, transcriptional or translational changes could separately result in functional loss of a gene, a pseudogenized SWS1 indicates a loss of dichromatic colour vision in bats. Thus, the same sensory trade-off appears to have repeatedly occurred in the two divergent lineages of HDC echolocators, and colour vision may have also been traded off against the infrared sense in vampire bats.
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Affiliation(s)
- Jinwei Wu
- Department of Ecology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China
| | - Hengwu Jiao
- Department of Ecology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China
| | - Nancy B Simmons
- Department of Mammalogy, American Museum of Natural History, New York, NY 10024, USA
| | - Qin Lu
- Department of Ecology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China
| | - Huabin Zhao
- Department of Ecology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China
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Hurtado N, D'Elía G. Taxonomy of the Genus Gardnerycteris (Chiroptera: Phyllostomidae). ACTA CHIROPTEROLOGICA 2018. [DOI: 10.3161/15081109acc2018.20.1.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Natali Hurtado
- Doctorado en Ciencias, Mención Ecología y Evolución, Universidad Austral de Chile, Campus Isla Teja s/n, Valdivia, Chile
- Departamento de Mastozoología, Museo de Historia Natural de la Universidad Nacional Mayor de San Marcos. Av. Arenales 1256, Lima 14, Lima, Peru
| | - Guillermo D'Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja s/n, Valdivia, Chile
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Hidden and cryptic species reflect parallel and correlated evolution in the phylogeny of the genus Callyntra (Coleoptera: Tenebrionidae) of Central Chile. Mol Phylogenet Evol 2018; 127:405-415. [PMID: 29702216 DOI: 10.1016/j.ympev.2018.04.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 04/02/2018] [Accepted: 04/15/2018] [Indexed: 11/23/2022]
Abstract
The origin of cryptic species has traditionally been associated with events of recent speciation, genetic constraints, selection of an adaptive character, sexual selection and/or convergent evolution. Species of the genus Callyntra inhabit coastal terraces, mountain slopes, and peaks; their elytral designs are associated with each of these habitats. However, cryptic species have been described within each of these habitats; the taxonomy of this group has been problematic, thus establishing the phylogenetic relationships in this group is fundamental to clarify the systematics and evolutionary patterns of Callyntra. We reconstructed the phylogeny of this group using two mitochondrial genes (COI, 16S) and one nuclear gene (Mp20). We also performed species delimitation using PTP based methods (PTP, mlPTP, bPTP) and GMYC, and evaluated the evolution of the elytral design related to habitat preference. The results showed a tree with five clades, that together with the different methods of species delimitation recovered the described species and suggested at least five new species. The elytral design and habitat preference showed phylogenetic signals. We propose a new classification based on monophyletic groups recovered by phylogenetic analyses. We also suggest that parallel evolution in different habitats and later stasis in the elytral design would be the cause of the origin of cryptic species in this group from central Chile.
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Kealy S, Beck R. Total evidence phylogeny and evolutionary timescale for Australian faunivorous marsupials (Dasyuromorphia). BMC Evol Biol 2017; 17:240. [PMID: 29202687 PMCID: PMC5715987 DOI: 10.1186/s12862-017-1090-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/22/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The order Dasyuromorphia is a diverse radiation of faunivorous marsupials, comprising >80 modern species in Australia and New Guinea. It includes dasyurids, the numbat (the myrmecobiid Myrmecobius fasciatus) and the recently extinct thylacine (the thylacinid Thylacinus cyncocephalus). There is also a diverse fossil record of dasyuromorphians and "dasyuromorphian-like" taxa known from Australia. We present the first total evidence phylogenetic analyses of the order, based on combined morphological and molecular data (including a novel set of 115 postcranial characters), to resolve relationships and calculate divergence dates. We use this information to analyse the diversification dynamics of modern dasyuromorphians. RESULTS Our morphology-only analyses are poorly resolved, but our molecular and total evidence analyses confidently resolve most relationships within the order, and are strongly congruent with recent molecular studies. Thylacinidae is the first family to diverge within the order, and there is strong support for four tribes within Dasyuridae (Dasyurini, Phascogalini, Planigalini and Sminthopsini). Among fossil taxa, Ankotarinja and Keeuna do not appear to be members of Dasyuromorphia, whilst Barinya and Mutpuracinus are of uncertain relationships within the order. Divergence dates calculated using total evidence tip-and-node dating are younger than both molecular node-dating and total evidence tip-dating, but appear more congruent with the fossil record and are relatively insensitive to calibration strategy. The tip-and-node divergence dates indicate that Dasyurini, Phascogalini and Sminthopsini began to radiate almost simultaneously during the middle-to-late Miocene (11.5-13.1 MYA; composite 95% HPD: 9.5-15.9 MYA); the median estimates for these divergences are shortly after a drop in global temperatures (the middle Miocene Climatic Transition), and coincide with a faunal turnover event in the mammalian fossil record of Australia. Planigalini radiated much later, during the latest Miocene to earliest Pliocene (6.5 MYA; composite 95% HPD: 4.4-8.9 MYA); the median estimates for these divergences coincide with an increase in grass pollen in the Australian palynological record that suggests the development of more open habitats, which are preferred by modern planigale species. CONCLUSIONS Our results provide a phylogenetic and temporal framework for interpreting the evolution of modern and fossil dasyuromorphians, but future progress will require a much improved fossil record.
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Affiliation(s)
- Shimona Kealy
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Acton, ACT Australia
| | - Robin Beck
- School of Environment and Life Sciences, University of Salford, Salford, M5 4WT UK
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Karanovic I, Sitnikova TY. Morphological and molecular diversity of Lake Baikal candonid ostracods, with description of a new genus. Zookeys 2017:19-56. [PMID: 28769732 PMCID: PMC5523182 DOI: 10.3897/zookeys.684.13249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/15/2017] [Indexed: 11/12/2022] Open
Abstract
Uncoupling between molecular and morphological evolution is common in many animal and plant lineages. This is especially frequent among groups living in ancient deep lakes, because these ecosystems promote rapid morphological diversification, and has already been demonstrated for Tanganyika cychlid fishes and Baikal amphipods. Ostracods are also very diverse in these ecosystems, with 107 candonid species described so far from Baikal, majority of them in the genera Candona Baird, 1845 and Pseudocandona Kaufmann, 1900. Here we study their morphological and molecular diversity based on four genes (two nuclear and two mitochondrial), 10 species from the lake, and 28 other species from around the world. The results of our phylogenetic analysis based on a concatenated data set, along with sequence diversity, support only two genetic lineages in the lake and indicate that a majority of the Baikal Candona and Pseudocandona species should be excluded from these genera. We describe a new genus, Mazepovacandonagen. n., to include five Baikal species, all redescribed here. We also amend the diagnosis for the endemic genus Baicalocandona Mazepova, 1972 and redescribe two species. Our study confirms an exceptional morphological diversity of Lake Baikal candonids and shows that both Baikal lineages are closely related to Candona, but only distantly to Pseudocandona.
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Affiliation(s)
- Ivana Karanovic
- Department of Life Science, College of Natural Science, Hanyang University, Seoul 133-791, South Korea; Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 49, 7001, Hobart, Tasmania, Australia
| | - Tatiana Ya Sitnikova
- Limnological Institute, Siberian Branch, Russian Academy of Sciences, P.O. Box 664033, Irkutsk, Russia
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Velazco PM, Soto-Centeno JA, Fleck DW, Voss RS, Simmons NB. A New Species of Nectar-Feeding Bat of the GenusHsunycteris(Phyllostomidae: Lonchophyllinae) from Northeastern Peru. AMERICAN MUSEUM NOVITATES 2017. [DOI: 10.1206/3881.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Paúl M. Velazco
- Division of Vertebrate Zoology (Mammalogy), American Museum of Natural History
| | | | - David W. Fleck
- Division of Anthropology, American Museum of Natural History
| | - Robert S. Voss
- Division of Vertebrate Zoology (Mammalogy), American Museum of Natural History
| | - Nancy B. Simmons
- Division of Vertebrate Zoology (Mammalogy), American Museum of Natural History
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Complete mitochondrial genomes are not necessarily more informative than individual mitochondrial genes to recover a well-established annelid phylogeny. GENE REPORTS 2016. [DOI: 10.1016/j.genrep.2016.07.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Bjarnason A, Soligo C, Elton S. Phylogeny, phylogenetic inference, and cranial evolution in pitheciids andAotus. Am J Primatol 2016; 79:1-11. [DOI: 10.1002/ajp.22621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 10/21/2016] [Accepted: 11/03/2016] [Indexed: 11/08/2022]
Affiliation(s)
| | | | - Sarah Elton
- Department of Anthropology; Durham University; Durham DH1 3LE
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Eyer PA, Leniaud L, Tinaut A, Aron S. Combined hybridization and mitochondrial capture shape complex phylogeographic patterns in hybridogenetic Cataglyphis desert ants. Mol Phylogenet Evol 2016; 105:251-262. [PMID: 27591172 DOI: 10.1016/j.ympev.2016.08.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 08/24/2016] [Accepted: 08/29/2016] [Indexed: 11/19/2022]
Abstract
Some species of Cataglyphis desert ants have evolved a hybridogenetic mode of reproduction at the social scale. In hybridogenetic populations, two distinct genetic lineages coexist. Non-reproductive offspring (workers) are hybrids of the two lineages, whereas sexual offspring (males and new queens) are produced by parthenogenesis and belong to the mother queen lineage. How this unusual reproductive system affects phylogeographic patterns and speciation processes remains completely unknown to date. Using one mitochondrial and four nuclear genes, we examined the phylogenetic relationships between three species of Cataglyphis (C. hispanica, C. humeya and C. velox) where complex DNA inheritance through social hybridogenesis may challenge phylogenetic inference. Our results bring two important insights. First, our data confirm a hybridogenetic mode of reproduction across the whole distribution range of the species C. hispanica. In contrast, they do not provide support for hybridogenesis in the populations sampled of C. humeya and C. velox. This suggests that these populations are not hybridogenetic, or that hybridogenesis is too recent to result in reciprocally monophyletic lineages on nuclear genes. Second, due to mitochondrial introgression between lineages (Darras and Aron, 2015), the faster-evolving COI marker is not lineage specific, hence, unsuitable to further investigate the segregation of lineages in the species studied. Different mitochondrial haplotypes occur in each locality sampled, resulting in strongly structured populations. This micro-allopatric structure leads to over-splitting species delimitation on mitochondrial gene, as every locality could potentially be considered a putative species; haploweb analyses of nuclear markers, however, yield species delimitations that are consistent with morphology. Overall, this study highlights how social hybridogenesis varies across species and shapes complex phylogeographic patterns.
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Affiliation(s)
- P A Eyer
- Evolutionary Biology & Ecology, CP 160/12, Université Libre de Bruxelles, 50, av. F.D. Roosevelt, B-1050 Brussels, Belgium.
| | - L Leniaud
- Evolutionary Biology & Ecology, CP 160/12, Université Libre de Bruxelles, 50, av. F.D. Roosevelt, B-1050 Brussels, Belgium
| | - A Tinaut
- Department of Animal Biology, Faculty of Sciences, University of Granada, E-18071 Granada, Spain
| | - S Aron
- Evolutionary Biology & Ecology, CP 160/12, Université Libre de Bruxelles, 50, av. F.D. Roosevelt, B-1050 Brussels, Belgium
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31
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Zou Z, Zhang J. Morphological and molecular convergences in mammalian phylogenetics. Nat Commun 2016; 7:12758. [PMID: 27585543 PMCID: PMC5025827 DOI: 10.1038/ncomms12758] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 07/29/2016] [Indexed: 12/30/2022] Open
Abstract
Phylogenetic trees reconstructed from molecular sequences are often considered more reliable than those reconstructed from morphological characters, in part because convergent evolution, which confounds phylogenetic reconstruction, is believed to be rarer for molecular sequences than for morphologies. However, neither the validity of this belief nor its underlying cause is known. Here comparing thousands of characters of each type that have been used for inferring the phylogeny of mammals, we find that on average morphological characters indeed experience much more convergences than amino acid sites, but this disparity is explained by fewer states per character rather than an intrinsically higher susceptibility to convergence for morphologies than sequences. We show by computer simulation and actual data analysis that a simple method for identifying and removing convergence-prone characters improves phylogenetic accuracy, potentially enabling, when necessary, the inclusion of morphologies and hence fossils for reliable tree inference. Morphological characters are generally thought to have higher rates of convergence than molecular characters. Here, Zou and Zhang provide empirical evidence for this assumption and devise a method to improve the accuracy of phylogenetic reconstruction through identifying and removing convergence-prone characters.
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Affiliation(s)
- Zhengting Zou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
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32
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Ottenburghs J, Megens HJ, Kraus RH, Madsen O, van Hooft P, van Wieren SE, Crooijmans RP, Ydenberg RC, Groenen MA, Prins HH. A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese. Mol Phylogenet Evol 2016; 101:303-313. [DOI: 10.1016/j.ympev.2016.05.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 04/27/2016] [Accepted: 05/20/2016] [Indexed: 11/26/2022]
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Baker RJ, Solari S, Cirranello A, Simmons NB. Higher Level Classification of Phyllostomid Bats with a Summary of DNA Synapomorphies. ACTA CHIROPTEROLOGICA 2016. [DOI: 10.3161/15081109acc2016.18.1.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Mans BJ, de Castro MH, Pienaar R, de Klerk D, Gaven P, Genu S, Latif AA. Ancestral reconstruction of tick lineages. Ticks Tick Borne Dis 2016; 7:509-35. [DOI: 10.1016/j.ttbdis.2016.02.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 01/26/2016] [Accepted: 02/02/2016] [Indexed: 01/15/2023]
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35
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Cirranello A, Simmons NB, Solari S, Baker RJ. Morphological Diagnoses of Higher-Level Phyllostomid Taxa (Chiroptera: Phyllostomidae). ACTA CHIROPTEROLOGICA 2016. [DOI: 10.3161/15081109acc2016.18.1.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Rojas D, Warsi OM, Dávalos LM. Bats (Chiroptera: Noctilionoidea) Challenge a Recent Origin of Extant Neotropical Diversity. Syst Biol 2016; 65:432-48. [DOI: 10.1093/sysbio/syw011] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 02/01/2016] [Indexed: 12/15/2022] Open
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37
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Dool SE, Puechmaille SJ, Foley NM, Allegrini B, Bastian A, Mutumi GL, Maluleke TG, Odendaal LJ, Teeling EC, Jacobs DS. Nuclear introns outperform mitochondrial DNA in inter-specific phylogenetic reconstruction: Lessons from horseshoe bats (Rhinolophidae: Chiroptera). Mol Phylogenet Evol 2016; 97:196-212. [PMID: 26826601 DOI: 10.1016/j.ympev.2016.01.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 01/07/2016] [Accepted: 01/08/2016] [Indexed: 01/22/2023]
Abstract
Despite many studies illustrating the perils of utilising mitochondrial DNA in phylogenetic studies, it remains one of the most widely used genetic markers for this purpose. Over the last decade, nuclear introns have been proposed as alternative markers for phylogenetic reconstruction. However, the resolution capabilities of mtDNA and nuclear introns have rarely been quantified and compared. In the current study we generated a novel ∼5kb dataset comprising six nuclear introns and a mtDNA fragment. We assessed the relative resolution capabilities of the six intronic fragments with respect to each other, when used in various combinations together, and when compared to the traditionally used mtDNA. We focused on a major clade in the horseshoe bat family (Afro-Palaearctic clade; Rhinolophidae) as our case study. This old, widely distributed and speciose group contains a high level of conserved morphology. This morphological stasis renders the reconstruction of the phylogeny of this group with traditional morphological characters complex. We sampled multiple individuals per species to represent their geographic distributions as best as possible (122 individuals, 24 species, 68 localities). We reconstructed the species phylogeny using several complementary methods (partitioned Maximum Likelihood and Bayesian and Bayesian multispecies-coalescent) and made inferences based on consensus across these methods. We computed pairwise comparisons based on Robinson-Foulds tree distance metric between all Bayesian topologies generated (27,000) for every gene(s) and visualised the tree space using multidimensional scaling (MDS) plots. Using our supported species phylogeny we estimated the ancestral state of key traits of interest within this group, e.g. echolocation peak frequency which has been implicated in speciation. Our results revealed many potential cryptic species within this group, even in taxa where this was not suspected a priori and also found evidence for mtDNA introgression. We demonstrated that by using just two introns one can recover a better supported species tree than when using the mtDNA alone, despite the shorter overall length of the combined introns. Additionally, when combining any single intron with mtDNA, we showed that the result is highly similar to the mtDNA gene tree and far from the true species tree and therefore this approach should be avoided. We caution against the indiscriminate use of mtDNA in phylogenetic studies and advocate for pilot studies to select nuclear introns. The selection of marker type and number is a crucial step that is best based on critical examination of preliminary or previously published data. Based on our findings and previous publications, we recommend the following markers to recover phylogenetic relationships between recently diverged taxa (<20 My) in bats and other mammals: ACOX2, COPS7A, BGN, ROGDI and STAT5A.
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Affiliation(s)
- Serena E Dool
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa; Zoological Institute and Museum, University of Greifswald, Soldmann-Straße 14, D-17487 Greifswald, Germany.
| | - Sebastien J Puechmaille
- Zoological Institute and Museum, University of Greifswald, Soldmann-Straße 14, D-17487 Greifswald, Germany; Midi-Pyrénées bat group (CREN-GCMP), Toulouse, France; School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Nicole M Foley
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | | | - Anna Bastian
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa.
| | - Gregory L Mutumi
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa.
| | - Tinyiko G Maluleke
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa.
| | - Lizelle J Odendaal
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa.
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - David S Jacobs
- Department of Biological Sciences, Animal Evolution and Systematics Group, University of Cape Town, Cape Town, South Africa.
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38
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Maires Hoppe JP, Ditchfield AD. Range extension of Mimon bennettii (Chiroptera: Phyllostomidae) in Brazil with comments on its systematics. MAMMALIA 2016. [DOI: 10.1515/mammalia-2015-0045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstractis widely distributed in South America. In Brazil, records are mainly concentrated in the Atlantic Forest and Cerrado biomes, although there are scattered occurrences in the Pantanal, Caatinga, and Amazonian biomes. In this study, we report the first occurrence of
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Heikkilä M, Mutanen M, Wahlberg N, Sihvonen P, Kaila L. Elusive ditrysian phylogeny: an account of combining systematized morphology with molecular data (Lepidoptera). BMC Evol Biol 2015; 15:260. [PMID: 26589618 PMCID: PMC4654798 DOI: 10.1186/s12862-015-0520-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/26/2015] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Ditrysia comprise close to 99 % of all butterflies and moths. The evolutionary relationships among the ditrysian superfamilies have received considerable attention in phylogenetic studies based on DNA and transcriptomic data, but the deepest divergences remain for large parts unresolved or contradictory. To obtain complementary insight into the evolutionary history of the clade, and to test previous hypotheses on the subdivision of Ditrysia based on morphology, we examine the morphology of larvae, pupae and adult males and females of 318 taxa representing nearly all ditrysian superfamilies and families. We present the most comprehensive morphological dataset on Ditrysia to date, consisting of over 500 morphological characters. The data are analyzed alone and combined with sequence data (one mitochondrial and seven nuclear protein-coding gene regions, sequenced from 422 taxa). The full dataset consists of 473 exemplar species. Analyses are performed using maximum likelihood methods, and parsimony methods for the morphological dataset. We explore whether combining morphological data and DNA-data can stabilize taxa that are unstable in phylogenetic studies based on genetic data only. RESULTS Morphological characters are found phylogenetically informative in resolving apical nodes (superfamilies and families), but characters serving as evidence of relatedness of larger assemblages are few. Results include the recovery of a monophyletic Tineoidea, Sesioidea and Cossoidea, and a stable position for some unstable taxa (e.g. Epipyropidae, Cyclotornidae, Urodoidea + Schreckensteinioidea). Several such taxa, however, remain unstable even though morphological characters indicate a position in the tree (e.g. Immidae). Evidence supporting affinities between clades are suggested, e.g. a novel larval synapomorphy for Tineidae. We also propose the synonymy of Tineodidae with Alucitidae, syn. nov. CONCLUSIONS The large morphological dataset provides information on the diversity and distribution of morphological traits in Ditrysia, and can be used in future research on the evolution of these traits, in identification keys and in identification of fossil Lepidoptera. The "backbone" of the phylogeny for Ditrysia remains largely unresolved. As previously proposed as an explanation for the scarcity of molecular signal in resolving the deeper nodes, this may be due to the rapid radiation of Ditrysia in the Cretaceous.
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Affiliation(s)
- Maria Heikkilä
- Finnish Museum of Natural History, Zoology Unit, University of Helsinki, PO Box 17, Helsinki, 00014, Finland.
| | - Marko Mutanen
- Department of Genetics and Physiology, University of Oulu, PO Box 3000, Oulu, 90014, Finland.
| | - Niklas Wahlberg
- Laboratory of Genetics, Department of Biology, University of Turku, Turku, 20014, Finland.
- Department of Biology, Lund University, 223 62, Lund, Sweden.
| | - Pasi Sihvonen
- University of Helsinki, Research Affairs, PO Box 33, Helsinki, 00014, Finland.
| | - Lauri Kaila
- Finnish Museum of Natural History, Zoology Unit, University of Helsinki, PO Box 17, Helsinki, 00014, Finland.
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Gamisch A, Fischer GA, Comes HP. Multiple independent origins of auto-pollination in tropical orchids (Bulbophyllum) in light of the hypothesis of selfing as an evolutionary dead end. BMC Evol Biol 2015; 15:192. [PMID: 26376901 PMCID: PMC4574068 DOI: 10.1186/s12862-015-0471-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 08/28/2015] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The transition from outcrossing to selfing has long been portrayed as an 'evolutionary dead end' because, first, reversals are unlikely and, second, selfing lineages suffer from higher rates of extinction owing to a reduced potential for adaptation and the accumulation of deleterious mutations. We tested these two predictions in a clade of Madagascan Bulbophyllum orchids (30 spp.), including eight species where auto-pollinating morphs (i.e., selfers, without a 'rostellum') co-exist with their pollinator-dependent conspecifics (i.e., outcrossers, possessing a rostellum). Specifically, we addressed this issue on the basis of a time-calibrated phylogeny by means of ancestral character reconstructions and within the state-dependent evolution framework of BiSSE (Binary State Speciation and Extinction), which allowed jointly estimating rates of transition, speciation, and extinction between outcrossing and selfing. RESULTS The eight species capable of selfing occurred in scattered positions across the phylogeny, with two likely originating in the Pliocene (ca. 4.4-3.1 Ma), one in the Early Pleistocene (ca. 2.4 Ma), and five since the mid-Pleistocene (ca. ≤ 1.3 Ma). We infer that this scattered phylogenetic distribution of selfing is best described by models including up to eight independent outcrossing-to-selfing transitions and very low rates of speciation (and either moderate or zero rates of extinction) associated with selfing. CONCLUSIONS The frequent and irreversible outcrossing-to-selfing transitions in Madagascan Bulbophyllum are clearly congruent with the first prediction of the dead end hypothesis. The inability of our study to conclusively reject or support the likewise predicted higher extinction rate in selfing lineages might be explained by a combination of methodological limitations (low statistical power of our BiSSE approach to reliably estimate extinction in small-sized trees) and evolutionary processes (insufficient time elapsed for selfers to go extinct). We suggest that, in these tropical orchids, a simple genetic basis of selfing (via loss of the 'rostellum') is needed to explain the strikingly recurrent transitions to selfing, perhaps reflecting rapid response to parallel and novel selective environments over Late Quaternary (≤ 1.3 Ma) time scales.
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Affiliation(s)
- Alexander Gamisch
- Department of Ecology and Evolution, University of Salzburg, A-5020, Salzburg, Austria.
| | | | - Hans Peter Comes
- Department of Ecology and Evolution, University of Salzburg, A-5020, Salzburg, Austria.
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Santana SE. Quantifying the effect of gape and morphology on bite force: biomechanical modelling and
in vivo
measurements in bats. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12522] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sharlene E. Santana
- Department of Biology and Burke Museum of Natural History and Culture University of Washington Box 315800 Seattle WA 98195‐1800USA
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Hand SJ, Lee DE, Worthy TH, Archer M, Worthy JP, Tennyson AJD, Salisbury SW, Scofield RP, Mildenhall DC, Kennedy EM, Lindqvist JK. Miocene Fossils Reveal Ancient Roots for New Zealand's Endemic Mystacina (Chiroptera) and Its Rainforest Habitat. PLoS One 2015; 10:e0128871. [PMID: 26083758 PMCID: PMC4470663 DOI: 10.1371/journal.pone.0128871] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 05/01/2015] [Indexed: 12/30/2022] Open
Abstract
The New Zealand endemic bat family Mystacinidae comprises just two Recent species referred to a single genus, Mystacina. The family was once more diverse and widespread, with an additional six extinct taxa recorded from Australia and New Zealand. Here, a new mystacinid is described from the early Miocene (19-16 Ma) St Bathans Fauna of Central Otago, South Island, New Zealand. It is the first pre-Pleistocene record of the modern genus and it extends the evolutionary history of Mystacina back at least 16 million years. Extant Mystacina species occupy old-growth rainforest and are semi-terrestrial with an exceptionally broad omnivorous diet. The majority of the plants inhabited, pollinated, dispersed or eaten by modern Mystacina were well-established in southern New Zealand in the early Miocene, based on the fossil record from sites at or near where the bat fossils are found. Similarly, many of the arthropod prey of living Mystacina are recorded as fossils in the same area. Although none of the Miocene plant and arthropod species is extant, most are closely related to modern taxa, demonstrating potentially long-standing ecological associations with Mystacina.
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Affiliation(s)
- Suzanne J. Hand
- School of Biological, Environmental and Earth Sciences, University of New South Wales, Sydney, New South Wales, Australia
- * E-mail:
| | - Daphne E. Lee
- Department of Geology, University of Otago, Dunedin, New Zealand
| | - Trevor H. Worthy
- School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
| | - Michael Archer
- School of Biological, Environmental and Earth Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Jennifer P. Worthy
- School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
| | | | - Steven W. Salisbury
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | | | | | | | - Jon K. Lindqvist
- Department of Geology, University of Otago, Dunedin, New Zealand
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Shi JJ, Rabosky DL. Speciation dynamics during the global radiation of extant bats. Evolution 2015; 69:1528-1545. [DOI: 10.1111/evo.12681] [Citation(s) in RCA: 202] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 05/04/2015] [Indexed: 02/03/2023]
Affiliation(s)
- Jeff J. Shi
- Department of Ecology and Evolutionary Biology and Museum of Zoology; University of Michigan; Ann Arbor Michigan 48109
| | - Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology; University of Michigan; Ann Arbor Michigan 48109
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Saldaña-Vázquez RA, Ruiz-Sanchez E, Herrera-Alsina L, Schondube JE. Digestive capacity predicts diet diversity in Neotropical frugivorous bats. J Anim Ecol 2015; 84:1396-404. [PMID: 25919065 DOI: 10.1111/1365-2656.12383] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 04/21/2015] [Indexed: 11/27/2022]
Abstract
1. Predicting the diet diversity of animals is important to basic and applied ecology. Knowledge of diet diversity in animals helps us understand niche partitioning, functional diversity and ecosystem services such as pollination, pest control and seed dispersal. 2. There is a negative relationship between the length of the digestive tract and diet diversity in animals; however, the role of digestive physiology in determining diet diversity has been ignored. This is especially important in vertebrates with powered flight because, unlike non-flying vertebrates, they have limitations that may constrain gut size. 3. Here, we evaluate the relationship between digestive capacity and diet diversity in Carollinae and Stenodermatinae frugivorous bats. These bats disperse the seeds of plants that are key to Neotropical forest regeneration. 4. Our results show that digestive capacity is a good predictor of diet diversity in Carollinae and Stenodermatinae frugivorous bats (R(2) = 0·77). 5. Surprisingly, the most phylogenetically closely related species were not similar in their digestive capacity or diet diversity. The lack of a phylogenetic signal for the traits evaluated implies differences in digestive physiology and diet in closely related species. 6. Our results highlight the predictive usefulness of digestive physiology for understanding the feeding ecology of animals.
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Affiliation(s)
- Romeo A Saldaña-Vázquez
- Red de Ecología Funcional, Instituto de Ecología A.C., Apdo. Postal 63, Xalapa, Ver., CP 91000, México.,Laboratorio de Ecología Funcional, Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Apdo. Postal 27-3 (Santa María de Guido), Morelia, Michoacán, 58089, México
| | - Eduardo Ruiz-Sanchez
- Red de Biodiversidad y Sistemática, Instituto de Ecología, A. C., Centro Regional de Bajío, Av. Lázaro Cárdenas 253, 61600, Pátzcuaro, Michoacán, México
| | - Leonel Herrera-Alsina
- Laboratorio de Macroecología, Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Apdo. Postal 27-3 (Santa María de Guido), Morelia, Michoacán, 58089, México
| | - Jorge E Schondube
- Laboratorio de Ecología Funcional, Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Apdo. Postal 27-3 (Santa María de Guido), Morelia, Michoacán, 58089, México
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Mans BJ, de Klerk D, Pienaar R, de Castro MH, Latif AA. Next-generation sequencing as means to retrieve tick systematic markers, with the focus on Nuttalliella namaqua (Ixodoidea: Nuttalliellidae). Ticks Tick Borne Dis 2015; 6:450-62. [DOI: 10.1016/j.ttbdis.2015.03.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 03/06/2015] [Accepted: 03/08/2015] [Indexed: 10/23/2022]
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Self CJ. Dental root size in bats with diets of different hardness. J Morphol 2015; 276:1065-74. [PMID: 26011087 DOI: 10.1002/jmor.20400] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 03/23/2015] [Accepted: 04/27/2015] [Indexed: 11/06/2022]
Abstract
The relationship between tooth roots and diet is relatively unexplored, although a logical relationship between harder diets and increased root surface area (RSA) is suggested. This study addresses the interaction between tooth morphology, diet, and bite force in small mammals, phyllostomid bats. Using micro computed tomography (microCT), tooth root morphology of two fruit-eating species (Carollia perspicillata and Chiroderma villosum) and two insect-eating species (Mimon bennettii and Macrotus californicus) was compared. These species did not differ in skull or estimated body size. Food hardness, rather than dietary classification, proved to be the strongest grouping factor, with the two insectivores and the seed-processing frugivore (C. villosum) having significantly larger RSAs. Bite force was estimated using skull measurements; bite force significantly correlated with tooth RSA but not with body size. Although the three durophagous species did exhibit larger crowns, the area of the occlusal surface did not vary among the four species. There was a linear relationship between root size and crown size, indicating that the roots were not expanded disproportionately; instead the entire tooth was larger in the hard diet species. MicroCT allows the nondestructive quantification of previously difficult-to-access tooth morphology; this method shows the potential for tooth roots to provide valuable dietary, behavioral, and ecological information in small mammals. J. Morphol. 276:1065-1074, 2015. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Casey J Self
- Department of Biology, University of Washington, Seattle, Washington
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Harrison LB, Larsson HCE. Among-Character Rate Variation Distributions in Phylogenetic Analysis of Discrete Morphological Characters. Syst Biol 2014; 64:307-24. [DOI: 10.1093/sysbio/syu098] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Luke B. Harrison
- Redpath Museum, McGill University, 859 Sherbrooke Street West Montreal, Quebec, Canada H3A 0C4 and 2Redpath Museum, McGill University, 859 Sherbrooke ST W, Montreal, Quebec, Canada H3A 0C4
| | - Hans C. E. Larsson
- Redpath Museum, McGill University, 859 Sherbrooke Street West Montreal, Quebec, Canada H3A 0C4 and 2Redpath Museum, McGill University, 859 Sherbrooke ST W, Montreal, Quebec, Canada H3A 0C4
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Martins FF, Puga CC, Beguelini MR, Morielle-Versute E, Vilamaior PS, Taboga SR. Comparative analysis of the male reproductive accessory glands of bat species from the five Brazilian Subfamilies of the family Phyllostomidae (Chiroptera). J Morphol 2014; 276:470-80. [DOI: 10.1002/jmor.20354] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/21/2014] [Accepted: 11/18/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Fabiane F. Martins
- Department of Biology; UNESP-Universidade Estadual Paulista; São José do Rio Preto São Paulo 15054-000 Brazil
| | - Cintia C.I. Puga
- Department of Biology; UNESP-Universidade Estadual Paulista; São José do Rio Preto São Paulo 15054-000 Brazil
| | - Mateus R. Beguelini
- Department of Biology; UNESP-Universidade Estadual Paulista; São José do Rio Preto São Paulo 15054-000 Brazil
| | - Eliana Morielle-Versute
- Department of Zoology and Botany; UNESP-Universidade Estadual Paulista; São José do Rio Preto São Paulo 15054-000 Brazil
| | - Patricia S.L. Vilamaior
- Department of Biology; UNESP-Universidade Estadual Paulista; São José do Rio Preto São Paulo 15054-000 Brazil
| | - Sebastião R. Taboga
- Department of Biology; UNESP-Universidade Estadual Paulista; São José do Rio Preto São Paulo 15054-000 Brazil
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Clairmont L, Mora EC, Fenton B. Morphology, Diet and Flower-visiting by Phyllostomid Bats in Cuba. Biotropica 2014. [DOI: 10.1111/btp.12118] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lindsey Clairmont
- Department of Biology; University of Western Ontario; 1151 Richmond St London ON N6A 5B7 Canada
| | - Emanuel C. Mora
- Department of Animal and Human Biology; Havana University; calle 25 No. 455 J e I Vedado La Habana Cuba
| | - Brock Fenton
- Department of Biology; University of Western Ontario; 1151 Richmond St London ON N6A 5B7 Canada
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Dávalos LM, Velazco PM, Warsi OM, Smits PD, Simmons NB. Integrating Incomplete Fossils by Isolating Conflicting Signal in Saturated and Non-Independent Morphological Characters. Syst Biol 2014; 63:582-600. [DOI: 10.1093/sysbio/syu022] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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