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Yap JYS, Rossetto M, Das S, Wilson PD, Beaumont LJ, Henry RJ. Tracking habitat or testing its suitability? Similar distributional patterns can hide very different histories of persistence versus nonequilibrium dynamics. Evolution 2022; 76:1209-1228. [PMID: 35304742 DOI: 10.1111/evo.14460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 12/20/2021] [Accepted: 12/29/2021] [Indexed: 01/21/2023]
Abstract
The expansions and contractions of a species' range in response to temporal changes in selective filters leave genetic signatures that can inform a more accurate reconstruction of their evolutionary history across the landscape. After a long period of continental decline, Australian rainforests settled into localized patterns of contraction or expansion during the climatic fluctuations of the Quaternary. The environmental impacts of recurring glacial and interglacial periods also intensified the arrival of new lineages from the Sunda shelf, and it can be expected that immigrant versus locally persistent taxa responded to environmental challenges in quantifiably different manner. To investigate how such differences impact on species' distribution, we contrast landscape genomic patterns and changes in habitat availability between a species with a long continental history on Doryphora sassafras and a Sunda-derived species (Toona ciliata), across a distributional overlap. Extensive landscape-level homogeneity across chloroplast and nuclear genomes for the Sunda-derived T. ciliata, characterize the genetic signature of a very recent invasion and a rapid southern "exploratory" expansion that had not been previously recorded in the Australian flora (i.e., of Gondwanan origin or Sahul-derived). In contrast, D. sassafras is consistent with other Sahul-derived species characterized by strong geographical divergence and regional differentiation. Interestingly, our findings suggest that admixture between genetically divergent populations during expansion events might be a contributing factor to the successful colonization of novel habitats. Overall, this study identifies some of the mechanisms regulating the rearrangements in species distributions and assemblage composition that follow major environmental shifts, and reminds us how a species' current range might not necessarily define species' habitat preference, with the consequence that estimates of past or future range might not always be reliable.
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Affiliation(s)
- Jia-Yee Samantha Yap
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden, Sydney, New South Wales, Australia.,Queensland Alliance of Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden, Sydney, New South Wales, Australia.,Queensland Alliance of Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - Sourav Das
- Department of Biological Sciences, Macquarie University, Brisbane, New South Wales, Australia.,Department of Forestry and Environmental Science, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Peter D Wilson
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden, Sydney, New South Wales, Australia.,Department of Biological Sciences, Macquarie University, Brisbane, New South Wales, Australia
| | - Linda J Beaumont
- Department of Biological Sciences, Macquarie University, Brisbane, New South Wales, Australia
| | - Robert J Henry
- Queensland Alliance of Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
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2
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Pynne J, Stober JM, Edelman AJ. Eastern Fox Squirrel (Sciurus niger) Occupancy in Fragmented Montane Longleaf Pine Forests. SOUTHEAST NAT 2020. [DOI: 10.1656/058.019.0221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- J.T. Pynne
- D.B. Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA 30602
| | - Jonathan M. Stober
- Shoal Creek Ranger District, Talladega National Forest, United States Forest Service, Heflin, AL 36264
| | - Andrew J. Edelman
- Department of Biology, University of West Georgia, Carrollton, GA 30118
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McRobie HR, Moncrief ND, Mundy NI. Multiple origins of melanism in two species of North American tree squirrel (Sciurus). BMC Evol Biol 2019; 19:140. [PMID: 31296164 PMCID: PMC6625063 DOI: 10.1186/s12862-019-1471-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/30/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND While our understanding of the genetic basis of convergent evolution has improved there are still many uncertainties. Here we investigate the repeated evolution of dark colouration (melanism) in eastern fox squirrels (Sciurus niger; hereafter "fox squirrels") and eastern gray squirrels (S. carolinensis; hereafter "gray squirrels"). RESULTS We show that convergent evolution of melanism has arisen by independent genetic mechanisms in two populations of the fox squirrel. In a western population, melanism is associated with a 24 bp deletion in the melanocortin-1-receptor gene (MC1RΔ24 allele), whereas in a south-eastern population, melanism is associated with a point substitution in the agouti signalling protein gene causing a Gly121Cys mutation. The MC1R∆24 allele is also associated with melanism in gray squirrels, and, remarkably, all the MC1R∆24 haplotypes are identical in the two species. Evolutionary analyses show that the MC1R∆24 haplotype is more closely related to other MC1R haplotypes in the fox squirrel than in the gray squirrel. Modelling supports the possibility of gene flow between the two species. CONCLUSIONS The presence of the MC1R∆24 allele and melanism in gray squirrels is likely due to introgression from fox squirrels, although we cannot completely rule out alternative hypotheses including introgression from gray squirrels to fox squirrels, or an ancestral polymorphism. Convergent melanism in these two species of tree squirrels has evolved by at least two and probably three different evolutionary routes.
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Affiliation(s)
- Helen R McRobie
- School of Life Sciences, Anglia Ruskin University, Cambridge, CB1 1PT, UK.
| | - Nancy D Moncrief
- Virginia Museum of Natural History, Martinsville, VA, 24112, USA
| | - Nicholas I Mundy
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
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Aghbolaghi MA, Ahmadzadeh F, Kiabi B, Keyghobadi N. The permanent inhabitant of the oak trees: phylogeography and genetic structure of the Persian squirrel (Sciurus anomalus). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz032] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Marzieh Asadi Aghbolaghi
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Faraham Ahmadzadeh
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Bahram Kiabi
- Department of Aquatic Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Nusha Keyghobadi
- Department of Biology, the University of Western Ontario, London, ON, Canada
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5
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Austin JD, Greene DU, Honeycutt RL, McCleery RA. Genetic evidence indicates ecological divergence rather than geographic barriers structure Florida fox squirrels. J Mammal 2018. [DOI: 10.1093/jmammal/gyy128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- James D Austin
- Department of Wildlife Ecology and Conservation, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Daniel U Greene
- Department of Wildlife Ecology and Conservation, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Rodney L Honeycutt
- Natural Science Division, Pepperdine University, Pacific Coast Highway, Malibu, CA, USA
| | - Robert A McCleery
- Department of Wildlife Ecology and Conservation, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
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Salvador de Jesús-Bonilla V, García-París M, Ibarra-Cerdeña CN, Zaldívar-Riverón A. Geographic patterns of phenotypic diversity in incipient species of North American blister beetles (Coleoptera: Meloidae) are not determined by species niches, but driven by demography along the speciation process. INVERTEBR SYST 2018. [DOI: 10.1071/is17072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Epicauta stigmata complex is a group of blister beetles composed of three parapatric or sympatric species that occur in central Mexico to southern USA: E. stigmata, E. uniforma and E. melanochroa. These species are morphologically very similar, and are mainly distinguished by body colour differences. Here we assessed whether phenotypic divergence in coloration patterns define evolutionary units within the complex. We studied the phylogenetic relationships, demographic history and concordances between morphological and ecological traits in the group. The complex apparently had a demographic history of recent population expansion during the last glaciation period 75000 to 9500 years ago. The three species show no reciprocal monophyly, and thus their allospecificity was not confirmed. The current distribution of haplotypes and the genetic divergences in these taxa can be explained by either recent mitochondrial introgression events caused by hybridisation or by incomplete lineage sorting. Colour pattern differences in the complex are not likely a product of local selection acting over a common genetic background. We suggest that phenotypic divergence in colour patterns during an incipient speciation process might be seen as an enhancing factor of cohesion within each of the three evolutionary units.
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Boone WW, McCleery RA, Reichert BE. Fox squirrel response to forest restoration treatments in longleaf pine. J Mammal 2017. [DOI: 10.1093/jmammal/gyx110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Tye CA, Greene DU, Giuliano WM, Mccleery RA. Using camera-trap photographs to identify individual fox squirrels (Sciurus niger) in the Southeastern United States. WILDLIFE SOC B 2015. [DOI: 10.1002/wsb.573] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Courtney A. Tye
- Department of Wildlife Ecology and Conservation; University of Florida; Gainesville FL 32611 USA
| | - Daniel U. Greene
- Department of Wildlife Ecology and Conservation; University of Florida; Gainesville FL 32611 USA
| | - William M. Giuliano
- Department of Wildlife Ecology and Conservation; University of Florida; Gainesville FL 32611 USA
| | - Robert A. Mccleery
- Department of Wildlife Ecology and Conservation; University of Florida; Gainesville FL 32611 USA
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Castellanos-Morales G, Gasca-Pineda J, Ceballos G, Ortega J. Genetic variation in a peripheral and declining population of black-tailed prairie dogs (Cynomys ludovicianus) from Mexico. J Mammal 2014. [DOI: 10.1644/12-mamm-a-099] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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McRobie HR, King LM, Fanutti C, Coussons PJ, Moncrief ND, Thomas APM. Melanocortin 1 receptor (MC1R) gene sequence variation and melanism in the gray (Sciurus carolinensis), fox (Sciurus niger), and red (Sciurus vulgaris) squirrel. J Hered 2014; 105:423-8. [PMID: 24534267 DOI: 10.1093/jhered/esu006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Sequence variations in the melanocortin 1 receptor (MC1R) gene are associated with melanism in many different species of mammals, birds, and reptiles. The gray squirrel (Sciurus carolinensis), found in the British Isles, was introduced from North America in the late 19th century. Melanism in the British gray squirrel is associated with a 24-bp deletion in the MC1R. To investigate the origin of this mutation, we sequenced the MC1R of 95 individuals including 44 melanic gray squirrels from both the British Isles and North America. Melanic gray squirrels of both populations had the same 24-bp deletion associated with melanism. Given the significant deletion associated with melanism in the gray squirrel, we sequenced the MC1R of both wild-type and melanic fox squirrels (Sciurus niger) (9 individuals) and red squirrels (Sciurus vulgaris) (39 individuals). Unlike the gray squirrel, no association between sequence variation in the MC1R and melanism was found in these 2 species. We conclude that the melanic gray squirrel found in the British Isles originated from one or more introductions of melanic gray squirrels from North America. We also conclude that variations in the MC1R are not associated with melanism in the fox and red squirrels.
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Affiliation(s)
- Helen R McRobie
- the Department of Life Sciences, Anglia Ruskin University, East Road, Cambridge CB1 1PT, UK
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Claytor SC, Muchlinski AE, Torres E. Multiple introductions of the eastern fox squirrel (Sciurus niger) in California. MITOCHONDRIAL DNA 2014; 26:583-92. [PMID: 24438286 DOI: 10.3109/19401736.2013.878903] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Eastern fox squirrels (Sciurus niger) have been introduced into California within the past 130 years. Recently, their range has been expanding at an alarming rate. Genetic diversity was assessed in 101 control region sequences of eastern fox squirrels from three geographic regions within California (Los Angeles County, Alameda and Contra Costa counties and Sacramento County) to determine if a single or multiple introductions occurred within California, as indicated by the detection of multiple haplotypes. A total of 11 haplotypes were discovered, with haplotypes rarely shared among geographic regions and no clustering by region in a haplotype network. This suggests that the introduction to different regions within California came from different source populations within the native range of the species. Haplotype diversity was highest in Los Angeles County. Due to a lack of phylogeographic structure in fox squirrels in their native range, it is difficult to identify the sources of all introductions.
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Affiliation(s)
- Sieara C Claytor
- Department of Biological Sciences, California State University , Los Angeles, CA , USA
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12
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Moncrief ND, Lack JB, Maldonado JE, Bryant KL, Edwards CW, Van Den Bussche RA. General lack of phylogeographic structure in two sympatric, forest obligate squirrels (Sciurus nigerandS. carolinensis). J Mammal 2012. [DOI: 10.1644/11-mamm-a-383.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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13
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Dixon MD. Post-Pleistocene range expansion of the recently imperiled eastern little brown bat (Myotis lucifugus lucifugus) from a single southern refugium. Ecol Evol 2012; 1:191-200. [PMID: 22393495 PMCID: PMC3287298 DOI: 10.1002/ece3.20] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/28/2011] [Accepted: 07/28/2011] [Indexed: 11/30/2022] Open
Abstract
Myotis lucifugus, once among the most widespread and common bats in North America, has been forecast to be extirpated east of the Rockies in as few as 16 years by the spread of white-nose syndrome. Recent genetic research has demonstrated that this species is paraphyletic and part of a broader species complex; however, only one lineage (Myotis lucifugus lucifugus [M. l. lucifugus]) is present in eastern North America. I used molecular tools and niche modeling to validate this and investigate the role that historical biogeography has played in the phylogenetic and population genetic structure of this species to determine if the eastern subspecies represents an evolutionarily distinct population. To establish the genetic structure within M. l. lucifugus, I densely sampled maternity colonies in Minnesota and sequenced 182 individuals for a portion of cytochrome b. Phylogenetic reconstruction and a haplotype network were used to infer the relationships among mitochondrial haplotypes. Population growth statistics were calculated to determine if there was evidence of significant expansion, and an environmental niche model (ENM) was constructed based on conditions during the last glacial maximum (LGM) to illustrate potential glacial refugia. All individuals derived from a single mitochondrial lineage. Genetic evidence points to population growth starting approximately 18 kya. ENM results show that there was likely a single large southern refugium extending across the southeastern United States and possibly several isolated refugia in western North America. Myotis lucifugus lucifugus likely maintained both a large range and a large population during the peaks of the glacial cycles, and its population appears to have expanded following the retreat of the Laurentide ice sheet. This imperiled lineage likely diverged in isolation from other members of the M. lucifugus/western long-eared Myotis during the Pleistocene.
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Tipton ML, Gignoux-Wolfsohn S, Stonebraker P, Chernoff B. Postglacial recolonization of eastern Blacknose Dace,Rhinichthys atratulus(Teleostei: Cyprinidae), through the gateway of New England. Ecol Evol 2012; 1:343-58. [PMID: 22393505 PMCID: PMC3287313 DOI: 10.1002/ece3.31] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 08/02/2011] [Accepted: 08/04/2011] [Indexed: 11/09/2022] Open
Abstract
During the last ice age, much of North America far south as 40°N was covered by glaciers (Hewitt 2000). About 20,000 years ago, as the glaciers retreated, the hydrologic landscape changed dramatically creating waterways for fish dispersal. The number of populations responsible for recolonization and the regions from which they recolonized are unknown for many freshwater fishes living in New England and southeastern Canada. The Blacknose Dace,Rhinichthys atratulus, is one of the freshwater fish species that recolonized this region. We hypothesize that the earliest deglaciated region, modern-day Connecticut, was recolonized byR. atratulusvia a single founding event by a single population. In this paper, we test this hypothesis phylogenetically with regard to the major drainage basins within Connecticut. The mitochondrial DNA exhibits low nucleotide diversity, high haplotype diversity, and a dominant haplotype found across the state. A small percentage of individuals in the Housatonic drainage basin, however, share a haplotype with populations in New York drainage basins, a haplotype not found elsewhere in Connecticut's drainage basins. We calculated a range for the rate of divergence for NADH dehydrogenase subunit 2 (nd2) and control region (ctr) of 4.43-6.76% and 3.84-8.48% per million years (my), respectively. While this range is higher than the commonly accepted rate of 2% for mitochondrial DNA, these results join a growing list of publications finding high rates of divergence for various taxa (Peterson and Masel 2009). The data support the conclusion that Connecticut as a whole was recolonized initially by a single founding event that came from a single refugium. Subsequently, the Housatonic basin alone experienced a secondary recolonization event.
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Pečnerová P, Martínková N. Evolutionary history of tree squirrels (Rodentia, Sciurini) based on multilocus phylogeny reconstruction. ZOOL SCR 2012. [DOI: 10.1111/j.1463-6409.2011.00528.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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