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Abstract
Whole genome sequences are beginning to revolutionize our understanding of phylogenetic relationships. Yet, even whole genome sequences can fail to resolve the evolutionary history of the most rapidly radiating lineages, where incomplete lineage sorting, standing genetic variation, introgression, and other factors obscure the phylogenetic history of the group. To overcome such challenges, one emerging strategy is to integrate results across different methods. Most such approaches have been implemented on reduced representation genomic data sets, but whole genomes should provide the maximum possible evidence approach. Here, we test the ability of single nucleotide polymorphisms extracted from whole genome resequencing data, implemented in an integrative genomic approach, to resolve key nodes in the phylogeny of the mbuna, rock-dwelling cichlid fishes of Lake Malaŵi, which epitomize the phylogenetic intractability that often accompanies explosive lineage diversification. This monophyletic radiation has diversified at an unparalleled rate into several hundred species in less than 2 million years. Using an array of phylogenomic methods, we consistently recovered four major clades of mbuna, but a large basal polytomy among them. Although introgression between clades apparently contributed to the challenge of phylogenetic reconstruction, reduction of the data set to nonintrogressed sites still did not help to resolve the basal polytomy. On the other hand, relationships among six congeneric species pairs were resolved without ambiguity, even in one case where existing data led us to predict that resolution would be difficult. We conclude that the bursts of diversification at the earliest stages of the mbuna radiation may be phylogenetically unresolvable, but other regions of the tree are phylogenetically clearly supported. Integration of multiple phylogenomic approaches will continue to increase confidence in relationships inferred from these and other whole-genome data sets. [Incomplete lineage sorting; introgression; linkage disequilibrium; multispecies coalescence; rapid radiation; soft polytomy.]
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2
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Wang C, Lu B, Li T, Liang G, Xu M, Liu X, Tao W, Zhou L, Kocher TD, Wang D. Nile Tilapia: A Model for Studying Teleost Color Patterns. J Hered 2021; 112:469-484. [PMID: 34027978 DOI: 10.1093/jhered/esab018] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/08/2021] [Indexed: 11/12/2022] Open
Abstract
The diverse color patterns of cichlid fishes play an important role in mate choice and speciation. Here we develop the Nile tilapia (Oreochromis niloticus) as a model system for studying the developmental genetics of cichlid color patterns. We identified 4 types of pigment cells: melanophores, xanthophores, iridophores and erythrophores, and characterized their first appearance in wild-type fish. We mutated 25 genes involved in melanogenesis, pteridine metabolism, and the carotenoid absorption and cleavage pathways. Among the 25 mutated genes, 13 genes had a phenotype in both the F0 and F2 generations. None of F1 heterozygotes had phenotype. By comparing the color pattern of our mutants with that of red tilapia (Oreochromis spp), a natural mutant produced during hybridization of tilapia species, we found that the pigmentation of the body and eye is controlled by different genes. Previously studied genes like mitf, kita/kitlga, pmel, tyrb, hps4, gch2, csf1ra, pax7b, and bco2b were proved to be of great significance for color patterning in tilapia. Our results suggested that tilapia, a fish with 4 types of pigment cells and a vertically barred wild-type color pattern, together with various natural and artificially induced color gene mutants, can serve as an excellent model system for study color patterning in vertebrates.
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Affiliation(s)
- Chenxu Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Baoyue Lu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Tao Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Guangyuan Liang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Mengmeng Xu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Xingyong Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Linyan Zhou
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Thomas D Kocher
- the Department of Biology, University of Maryland, College Park, MD
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
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3
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Body-generated hydrodynamic flows influence male–male contests and female mate choice in a freshwater fish. Anim Behav 2020. [DOI: 10.1016/j.anbehav.2020.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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4
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Losilla M, Luecke DM, Gallant JR. The transcriptional correlates of divergent electric organ discharges in Paramormyrops electric fish. BMC Evol Biol 2020; 20:6. [PMID: 31918666 PMCID: PMC6953315 DOI: 10.1186/s12862-019-1572-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 12/24/2019] [Indexed: 01/10/2023] Open
Abstract
Background Understanding the genomic basis of phenotypic diversity can be greatly facilitated by examining adaptive radiations with hypervariable traits. In this study, we focus on a rapidly diverged species group of mormyrid electric fish in the genus Paramormyrops, which are characterized by extensive phenotypic variation in electric organ discharges (EODs). The main components of EOD diversity are waveform duration, complexity and polarity. Using an RNA-sequencing based approach, we sought to identify gene expression correlates for each of these EOD waveform features by comparing 11 specimens of Paramormyrops that exhibit variation in these features. Results Patterns of gene expression among Paramormyrops are highly correlated, and 3274 genes (16%) were differentially expressed. Using our most restrictive criteria, we detected 145–183 differentially expressed genes correlated with each EOD feature, with little overlap between them. The predicted functions of several of these genes are related to extracellular matrix, cation homeostasis, lipid metabolism, and cytoskeletal and sarcomeric proteins. These genes are of significant interest given the known morphological differences between electric organs that underlie differences in the EOD waveform features studied. Conclusions In this study, we identified plausible candidate genes that may contribute to phenotypic differences in EOD waveforms among a rapidly diverged group of mormyrid electric fish. These genes may be important targets of selection in the evolution of species-specific differences in mate-recognition signals.
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Affiliation(s)
- Mauricio Losilla
- Department of Integrative Biology, Michigan State University, East Lansing, MI, 48824, USA.,Graduate Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - David Michael Luecke
- Department of Integrative Biology, Michigan State University, East Lansing, MI, 48824, USA.,Graduate Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - Jason R Gallant
- Department of Integrative Biology, Michigan State University, East Lansing, MI, 48824, USA. .,Graduate Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48824, USA.
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5
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Gottsberger B, Mayer F. Dominance effects strengthen premating hybridization barriers between sympatric species of grasshoppers (Acrididae, Orthoptera). J Evol Biol 2019; 32:921-930. [PMID: 31127969 PMCID: PMC6851987 DOI: 10.1111/jeb.13490] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/13/2019] [Accepted: 05/21/2019] [Indexed: 01/23/2023]
Abstract
Sexual selection can lead to the rapid evolution of premating hybridization barriers and allows accelerated diversification and speciation within an evolutionary lineage. Especially during early stages of divergence, hybridization may impede further divergence, which strongly depends on the reproductive success of hybrids. Behavioural sterility of hybrids can limit or even prevent homogenizing gene flow. In this study, we investigated the attractiveness of male courtship songs for females of the grasshopper species Chorthippus biguttulus and C. brunneus and their interspecific F1 and F2 hybrids. Song preferences of females of both species are highly species specific and differ in three parameters: shape of the preference function, preference for syllable pattern and phrase duration. F1 hybrid females of both reciprocal crosses as well as F2 hybrid females resembled closely pure C. biguttulus females in respect of shape of the preference function and preference for syllable pattern, while preference for phrase duration showed an intermediate expression. This resulted in song preferences of hybrid females that closely resembled those of one parental species, that is C. biguttulus females. Such strong dominance effects were rarely reported so far. They represent an effective barrier limiting gene flow between the two species, since hybrid females will backcross to only one parental species and discriminate against hybrid males, which are behaviourally sterile. Such taxon-specific modes of inheritance may have facilitated the rapid divergence of acoustically communicating grasshoppers of the species group of Chorthippus biguttulus. Our findings have novel implications on the expression of neuronal filters and the evolution of complex courtship signals.
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Affiliation(s)
- Brigitte Gottsberger
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Frieder Mayer
- Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
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6
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Groot AT, van Wijk M, Villacis-Perez E, Kuperus P, Schöfl G, van Veldhuizen D, Heckel DG. Within-population variability in a moth sex pheromone blend, part 2: selection towards fixation. ROYAL SOCIETY OPEN SCIENCE 2019; 6:182050. [PMID: 31032049 PMCID: PMC6458377 DOI: 10.1098/rsos.182050] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
To understand how variation in sexual communication systems evolves, the genetic architecture underlying sexual signals and responses needs to be identified. Especially in animals where mating signals are important for mate recognition, and signals and responses are governed by independently assorting genes, it is difficult to envision how signals and preferences can (co)evolve. Moths are a prime example of such animals. In the noctuid moth Heliothis virescens, we found within-population variation in the female pheromone. In previous selection experiments followed by quantitative trait locus (QTL) analysis and expression analysis of candidate desaturase genes, we developed a model involving a trans-acting repressor of the delta-11-desaturase. In our current study with new selection lines, we fixed the most extreme phenotype and found a single underlying mutation: a premature stop codon in the first coding exon of delta-11-desaturase, which we could trace back to its origin in the laboratory. Interestingly, we found no pleiotropic effects of this knock-out mutation on the male physiological or behavioural response, or on growth or fertility. This finding is in contrast to Drosophila melanogaster, where a single desaturase gene affects both female pheromone production and male behavioural response, but similar to other Lepidoptera where these traits are under independent genetic control. To our knowledge, this is the first time that a single point mutation has been identified that underlies the phenotypic variation in the pheromone signal of a moth.
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Affiliation(s)
- Astrid T. Groot
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Department Entomology, Max Planck Institute for Chemical Ecology, Hans Knoell Strasse 8, 07745 Jena, Germany
| | - Michiel van Wijk
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Ernesto Villacis-Perez
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Peter Kuperus
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Gerhard Schöfl
- Department Entomology, Max Planck Institute for Chemical Ecology, Hans Knoell Strasse 8, 07745 Jena, Germany
| | - Dennis van Veldhuizen
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - David G. Heckel
- Department Entomology, Max Planck Institute for Chemical Ecology, Hans Knoell Strasse 8, 07745 Jena, Germany
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Hulsey CD, Holzman R, Meyer A. Dissecting a potential spandrel of adaptive radiation: Body depth and pectoral fin ecomorphology coevolve in Lake Malawi cichlid fishes. Ecol Evol 2018; 8:11945-11953. [PMID: 30598789 PMCID: PMC6303698 DOI: 10.1002/ece3.4651] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 09/22/2018] [Accepted: 10/01/2018] [Indexed: 01/11/2023] Open
Abstract
The evolution of body shape reflects both the ecological factors structuring organismal diversity as well as an organism's underlying anatomy. For instance, body depth in fishes is thought to determine their susceptibility to predators, attractiveness to mates, as well as swimming performance. However, the internal anatomy influencing diversification of body depth has not been extensively examined, and changes in body depth could arise as a by-product of functional changes in other anatomical structures. Using an improved phylogenetic hypothesis for a diverse set of Lake Malawi cichlid fishes, we tested the evolutionary association between body depth and the height of the pectoral girdle. To refine the functional importance of the observed substantial correlation, we also tested the coevolution of pectoral girdle height and pectoral fin area. The extensive coevolution of these traits suggests body depth in fishes like the Lake Malawi cichlids could diverge simply as a by-product of being tightly linked to ecomorphological divergence in other functional morphological structures like the pectoral fins.
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Affiliation(s)
| | - Roi Holzman
- School of Zoology, Faculty of Life scienceTel Aviv University, Tel Aviv, Israel and The Inter‐University Institute for Marine SciencesEilatIsrael
| | - Axel Meyer
- Department of BiologyUniversity of KonstanzKonstanzGermany
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Robertson JM, Nava R, Vega A, Kaiser K. Uniformity in premating reproductive isolation along an intraspecific cline. Curr Zool 2018; 64:641-652. [PMID: 30323843 PMCID: PMC6178793 DOI: 10.1093/cz/zox066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/10/2017] [Indexed: 11/17/2022] Open
Abstract
Premating reproductive isolation (RI) may reduce gene flow across populations that have differentiated in traits important for mate choice. Examining RI across genetic and phenotypic clines can inform the fundamental evolutionary processes that underlie population and lineage differentiation. We conducted female mate-choice studies across an intraspecific red-eyed treefrog cline in Costa Rica and Panama with 2 specific aims: (1) to characterize RI across the cline and examine the relationship between premating RI and genetic and phenotypic distance and (2) to evaluate our results within a broader evolutionary and taxonomic perspective through examination of other RI studies. We found that female red-eyed treefrogs prefer local males relative to non-local males, indicating that some premating RI has evolved in this system, but that preference strength is not associated with phenotypic or geographic distance. Our analysis of 65 other studies revealed no clear pattern between the strength of RI and geographic distribution (allopatry, parapatry, cline) or phenotypic distance, but revealed extreme variation and overlap in levels of intra- and interspecific levels of RI. This work contributes to a growing body of literature that examines intraspecific RI across a cline to understand the selective processes that shape evolutionary patterns at the earliest stages of divergence.
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Affiliation(s)
- Jeanne Marie Robertson
- Department of Biology, California State University, Northridge, 18111 Nordhoff Street, Northridge, CA, USA.,Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, CA, USA
| | - Roman Nava
- Department of Biology, California State University, Northridge, 18111 Nordhoff Street, Northridge, CA, USA.,Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, USA
| | - Andrés Vega
- AMBICOR, 400 E., 75 S., 75 E. de la Municipalidad de Tibas, Tibas, Costa Rica
| | - Kristine Kaiser
- Department of Biology, California State University, Northridge, 18111 Nordhoff Street, Northridge, CA, USA.,Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, CA, USA
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Svensson O, Woodhouse K, van Oosterhout C, Smith A, Turner GF, Seehausen O. The genetics of mate preferences in hybrids between two young and sympatric Lake Victoria cichlid species. Proc Biol Sci 2018; 284:rspb.2016.2332. [PMID: 28202807 DOI: 10.1098/rspb.2016.2332] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/24/2017] [Indexed: 12/29/2022] Open
Abstract
The genetic architecture of mate preferences is likely to affect significant evolutionary processes, including speciation and hybridization. Here, we investigate laboratory hybrids between a pair of sympatric Lake Victoria cichlid fish species that appear to have recently evolved from a hybrid population between similar predecessor species. The species demonstrate strong assortative mating in the laboratory, associated with divergent male breeding coloration (red dorsum versus blue). We show in a common garden experiment, using DNA-based paternity testing, that the strong female mate preferences among males of the two species are fully recovered in a large fraction of their F2 hybrid generation. Individual hybrid females often demonstrated consistent preferences in multiple mate choice trials (more than or equal to five) across a year or more. This result suggests that female mate preference is influenced by relatively few major genes or genomic regions. These preferences were not changed by experience of a successful spawning event with a male of the non-preferred species in a no-choice single-male trial. We found no evidence for imprinting in the F2 hybrids, although the F1 hybrid females may have been imprinted on their mothers. We discuss this nearly Mendelian inheritance of consistent innate mate preferences in the context of speciation theory.
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Affiliation(s)
- Ola Svensson
- School of Environmental Sciences, University of Hull, Hull HU6 7RX, UK
| | - Katie Woodhouse
- School of Environmental Sciences, University of Hull, Hull HU6 7RX, UK
| | | | - Alan Smith
- School of Environmental Sciences, University of Hull, Hull HU6 7RX, UK
| | - George F Turner
- School of Environmental Sciences, University of Hull, Hull HU6 7RX, UK
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Seestrasse 79, 6047 Kastanienbaum, Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
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10
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Husemann M, Tobler M, McCauley C, Ding B, Danley PD. Body shape differences in a pair of closely related Malawi cichlids and their hybrids: Effects of genetic variation, phenotypic plasticity, and transgressive segregation. Ecol Evol 2017. [PMID: 28649345 PMCID: PMC5478046 DOI: 10.1002/ece3.2823] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Phenotypic differences may have genetic and plastic components. Here, we investigated the contributions of both for differences in body shape in two species of Lake Malawi cichlids using wild-caught specimens and a common garden experiment. We further hybridized the two species to investigate the mode of gene action influencing body shape differences and to examine the potential for transgressive segregation. We found that body shape differences between the two species observed in the field are maintained after more than 10 generations in a standardized environment. Nonetheless, both species experienced similar changes in the laboratory environment. Our hybrid cross experiment confirmed that substantial variation in body shape appears to be genetically determined. The data further suggest that the underlying mode of gene action is complex and cannot be explained by simple additive or additive-dominance models. Transgressive phenotypes were found in the hybrid generations, as hybrids occupied significantly more morphospace than both parentals combined. Further, the body shapes of transgressive individuals resemble the body shapes observed in other Lake Malawi rock-dwelling genera. Our findings indicate that body shape can respond to selection immediately, through plasticity, and over longer timescales through adaptation. In addition, our results suggest that hybridization may have played an important role in the diversification of Lake Malawi cichlids through creating new phenotypic variation.
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Affiliation(s)
- Martin Husemann
- Centrum für Naturkunde University of Hamburg Hamburg Germany.,Biology Department Baylor University Waco TX USA
| | - Michael Tobler
- Division of Biology Kansas State University Manhattan KS USA
| | - Cagney McCauley
- Biology Department Baylor University Waco TX USA.,Department of Biological Sciences Institute of Applied Sciences University of North Texas 282 Cr 332 Rosebud Denton TX USA
| | - Baoqing Ding
- Biology Department Baylor University Waco TX USA.,Department of Ecology and Evolutionary Biology University of Connecticut Storrs CT USA
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11
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Husemann M, Nguyen R, Ding B, Danley PD. A genetic demographic analysis of Lake Malawi rock-dwelling cichlids using spatio-temporal sampling. Mol Ecol 2015; 24:2686-701. [DOI: 10.1111/mec.13205] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 04/08/2015] [Accepted: 04/13/2015] [Indexed: 02/03/2023]
Affiliation(s)
- Martin Husemann
- Biology Department; Baylor University; One Bear Place #97388 Waco TX 76798 USA
- Department of General Zoology; Institute of Biology; Martin-Luther University Halle-Wittenberg; Hoher Weg 8 Halle (Saale) D-06120 Germany
| | - Rachel Nguyen
- Biology Department; Baylor University; One Bear Place #97388 Waco TX 76798 USA
| | - Baoqing Ding
- Biology Department; Baylor University; One Bear Place #97388 Waco TX 76798 USA
| | - Patrick D. Danley
- Biology Department; Baylor University; One Bear Place #97388 Waco TX 76798 USA
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