1
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Fenker J, Melville J, Moritz C. Dragons in the tropics - Phylogeography and speciation in Diporiphora lizards and common geographic breaks in co-distributed taxa. Mol Phylogenet Evol 2024; 197:108090. [PMID: 38723791 DOI: 10.1016/j.ympev.2024.108090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 12/20/2023] [Accepted: 05/04/2024] [Indexed: 05/25/2024]
Abstract
Co-distributed taxa can respond both similarly or differently to the same climatic and geological events, resulting in a range of phylogeographic patterns across the region. Using a nested approach on a taxonomically diverse yet morphologically conservative group of agamid lizards, we first aimed to evaluate more precisely the extent of phylogeographic structuring within the genus. Then, focusing on four lineages within the more widespread species, we assessed the impact of biogeographic barriers on phylogeographic structuring and demographic history of species, comparing to patterns previously observed in co-distributed taxa. These species occur in the Australian Monsoonal Tropics, a vast tropical savanna system with high richness and endemism associated with environmental heterogeneity and past climate fluctuations. The employment of genomic data helped to determine the relationships between specific taxa that were previously difficult to place. We found a local influence of biogeographic and climatic breaks on population dynamics, analogous to other species. We detected high levels of population structure in the West Kimberley and Arnhem Plateau, which are already known for high endemism. However, we also highlighted unique lineages in areas that have been overlooked until recently, in the South Kimberley and West Top End. Climatic and geographical features in the Arnhem Plateau act as a soft barrier between populations in the east and west regions of the Top End. These observations reflect patterns observed for other vertebrates across this rich biome, indicating how climatic variation, species' ecology, and landscape features interact to shape regional diversity and endemism.
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Affiliation(s)
- Jessica Fenker
- Division of Ecology & Evolution, Research School of Biology, Australian National University, 46 Sullivans Creek Road, Acton 2601, Canberra, ACT, Australia; Department of Sciences, Museums Victoria, Melbourne Museum, 11 Nicholson StreetCarlton 3053, Melbourne, VIC, Australia.
| | - Jane Melville
- Department of Sciences, Museums Victoria, Melbourne Museum, 11 Nicholson StreetCarlton 3053, Melbourne, VIC, Australia
| | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, Australian National University, 46 Sullivans Creek Road, Acton 2601, Canberra, ACT, Australia
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2
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Parkin T, Donnellan SC, Parkin B, Shea GM, Rowley JJL. Phylogeography, hybrid zones and contemporary species boundaries in the south-eastern Australian smooth frogs (Anura: Myobatrachidae: Geocrinia). Mol Phylogenet Evol 2023; 189:107934. [PMID: 37769826 DOI: 10.1016/j.ympev.2023.107934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
Paleo-climatic fluctuations have driven episodic changes in species distributions, providing opportunities for populations to diverge in isolation and hybridise following secondary contact. Studies of phylogeographic diversity and patterns of gene flow across hybrid zones can provide insight into contemporary species boundaries and help to inform taxonomic and conservation inferences. Here we explore geographic diversity within the acoustically divergent yet morphologically conserved south-eastern Australian smooth frog complex and assess gene flow across a narrow hybrid zone using mitochondrial nucleotide sequences and nuclear genome-wide single nucleotide polymorphisms. Our analyses reveal the presence of an evolutionarily distinct taxon restricted to the Otway Plains and Ranges, Victoria, which forms a narrow (9-30 km wide), spatiotemporally stable (>50 years) hybrid zone with Geocrinia laevis, which we describe herein as a new species.
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Affiliation(s)
- Thomas Parkin
- Australian Museum Research Institute, Sydney NSW 2010, Australia.
| | | | - Benjamin Parkin
- Australian Museum Research Institute, Sydney NSW 2010, Australia
| | - Glenn M Shea
- Australian Museum Research Institute, Sydney NSW 2010, Australia; Sydney School of Veterinary Science B01, University of Sydney, NSW 2006, Australia
| | - Jodi J L Rowley
- Australian Museum Research Institute, Sydney NSW 2010, Australia; University of New South Wales, Sydney NSW 2052, Australia
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3
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Hyman IT, Köhler F. Homoplasy in shells discombobulated the taxonomy: revision of the larger helicarionid land snails of northern Queensland, Australia (Stylommatophora: Helicarionidae). J NAT HIST 2022. [DOI: 10.1080/00222933.2022.2136017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Isabel T. Hyman
- Department of Malacology, Australian Museum, Sydney, Australia
| | - Frank Köhler
- Department of Malacology, Australian Museum, Sydney, Australia
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4
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Hua X, Herdha T, Burden C. Protracted speciation under the state-dependent speciation and extinction approach. Syst Biol 2022; 71:1362-1377. [PMID: 35699529 PMCID: PMC9558848 DOI: 10.1093/sysbio/syac041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 05/16/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022] Open
Abstract
How long does speciation take? The answer to this important question in evolutionary biology lies in the genetic difference not only among species, but also among lineages within each species. With the advance of genome sequencing in non-model organisms and the statistical tools to improve accuracy in inferring evolutionary histories among recently diverged lineages, we now have the lineage-level trees to answer these questions. However, we do not yet have an analytical tool for inferring speciation processes from these trees. What is needed is a model of speciation processes that generates both the trees and species identities of extant lineages. The model should allow calculation of the probability that certain lineages belong to certain species and have an evolutionary history consistent with the tree. Here, we propose such a model and test the model performance on both simulated data and real data. We show that maximum-likelihood estimates of the model are highly accurate and give estimates from real data that generate patterns consistent with observations. We discuss how to extend the model to account for different rates and types of speciation processes across lineages in a species group. By linking evolutionary processes on lineage level to species level, the model provides a new phylogenetic approach to study not just when speciation happened, but how speciation happened. [Micro–macro evolution; Protracted birth–death process; speciation completion rate; SSE approach.]
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Affiliation(s)
- Xia Hua
- Mathematical Sciences Institute, Australian National University, Canberra ACT 0200 Australia
| | - Tyara Herdha
- Mathematical Sciences Institute, Australian National University, Canberra ACT 0200 Australia
| | - Conrad Burden
- Mathematical Sciences Institute, Australian National University, Canberra ACT 0200 Australia
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5
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Shepherd L, Simon C, Langton-Myers S, Morgan-Richards M. Insights into Aotearoa New Zealand’s biogeographic history provided by the study of natural hybrid zones. J R Soc N Z 2022. [DOI: 10.1080/03036758.2022.2061020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Lara Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
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6
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Genomic Screening to Identify Food Trees Potentially Dispersed by Precolonial Indigenous Peoples. Genes (Basel) 2022; 13:genes13030476. [PMID: 35328030 PMCID: PMC8954434 DOI: 10.3390/genes13030476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 02/22/2022] [Accepted: 03/03/2022] [Indexed: 12/04/2022] Open
Abstract
Over millennia, Indigenous peoples have dispersed the propagules of non-crop plants through trade, seasonal migration or attending ceremonies; and potentially increased the geographic range or abundance of many food species around the world. Genomic data can be used to reconstruct these histories. However, it can be difficult to disentangle anthropogenic from non-anthropogenic dispersal in long-lived non-crop species. We developed a genomic workflow that can be used to screen out species that show patterns consistent with faunal dispersal or long-term isolation, and identify species that carry dispersal signals of putative human influence. We used genotyping-by-sequencing (DArTseq) and whole-plastid sequencing (SKIMseq) to identify nuclear and chloroplast Single Nucleotide Polymorphisms in east Australian rainforest trees (4 families, 7 genera, 15 species) with large (>30 mm) or small (<30 mm) edible fruit, either with or without a known history of use by Indigenous peoples. We employed standard population genetic analyses to test for four signals of dispersal using a limited and opportunistically acquired sample scheme. We expected different patterns for species that fall into one of three broadly described dispersal histories: (1) ongoing faunal dispersal, (2) post-megafauna isolation and (3) post-megafauna isolation followed by dispersal of putative human influence. We identified five large-fruited species that displayed strong population structure combined with signals of dispersal. We propose coalescent methods to investigate whether these genomic signals can be attributed to post-megafauna isolation and dispersal by Indigenous peoples.
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7
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Discovery of cryptic plant diversity on the rooftops of the Alps. Sci Rep 2021; 11:11128. [PMID: 34045566 PMCID: PMC8159976 DOI: 10.1038/s41598-021-90612-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/04/2021] [Indexed: 11/08/2022] Open
Abstract
High elevation temperate mountains have long been considered species poor owing to high extinction or low speciation rates during the Pleistocene. We performed a phylogenetic and population genomic investigation of an emblematic high-elevation plant clade (Androsace sect. Aretia, 31 currently recognized species), based on plant surveys conducted during alpinism expeditions. We inferred that this clade originated in the Miocene and continued diversifying through Pleistocene glaciations, and discovered three novel species of Androsace dwelling on different bedrock types on the rooftops of the Alps. This highlights that temperate high mountains have been cradles of plant diversity even during the Pleistocene, with in-situ speciation driven by the combined action of geography and geology. Our findings have an unexpected historical relevance: H.-B. de Saussure likely observed one of these species during his 1788 expedition to the Mont Blanc and we describe it here, over two hundred years after its first sighting.
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8
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Menchetti M, Talavera G, Cini A, Salvati V, Dincă V, Platania L, Bonelli S, Balletto E, Vila R, Dapporto L. Two ways to be endemic. Alps and Apennines are different functional refugia during climatic cycles. Mol Ecol 2021; 30:1297-1310. [PMID: 33421216 DOI: 10.1111/mec.15795] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/21/2020] [Accepted: 01/04/2021] [Indexed: 01/03/2023]
Abstract
Endemics co-occur because they evolved in situ and persist regionally or because they evolved ex situ and later dispersed to shared habitats, generating evolutionary or ecological endemicity centres, respectively. We investigate whether different endemicity centres can intertwine in the region ranging from Alps to Sicily, by studying their butterfly fauna. We gathered an extensive occurrence data set for butterflies of the study area (27,123 records, 269 species, in cells of 0.5 × 0.5 degrees of latitude-longitude). We applied molecular-based delimitation methods (GMYC model) to 26,557 cytochrome c oxidase subunit 1 (COI) sequences of Western Palearctic butterflies. We identified entities based on molecular delimitations and/or the checklist of European butterflies and objectively attributed occurrences to their most probable entity. We obtained a zoogeographic regionalisation based on the 69 endemics of the area. Using phylogenetic ANOVA we tested if endemics from different centres differ from each other and from nonendemics for key ecological traits and divergence time. Endemicity showed high incidence in the Alps and Southern Italy. The regionalisation separated the Alps from the Italian Peninsula and Sicily. The endemics of different centres showed a high turnover and differed in phylogenetic distances, phenology and distribution traits. Endemics are on average younger than nonendemics and the Peninsula-Sicily endemics also have lower variance in divergence than those from the Alps. The observed variation identifies Alpine endemics as paleoendemics, now occupying an ecological centre, and the Peninsula-Sicily ones as neoendemics, that diverged in the region since the Pleistocene. The results challenge the common view of the Alpine-Apennine area as a single "Italian refugium".
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Affiliation(s)
- Mattia Menchetti
- ZEN Laboratory, Dipartimento di Biologia, Università degli Studi di Firenze, Sesto Fiorentino, Italy.,Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
| | - Alessandro Cini
- ZEN Laboratory, Dipartimento di Biologia, Università degli Studi di Firenze, Sesto Fiorentino, Italy.,Centre for Biodiversity & Environment Research, University College London, London, UK
| | - Vania Salvati
- ZEN Laboratory, Dipartimento di Biologia, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Vlad Dincă
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Leonardo Platania
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Simona Bonelli
- ZOOLAB, Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Turin, Italy
| | - Emilio Balletto
- ZOOLAB, Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Turin, Italy
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Leonardo Dapporto
- ZEN Laboratory, Dipartimento di Biologia, Università degli Studi di Firenze, Sesto Fiorentino, Italy
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9
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Dean LL, Dunstan HR, Reddish A, MacColl ADC. Courtship behavior, nesting microhabitat, and assortative mating in sympatric stickleback species pairs. Ecol Evol 2021; 11:1741-1755. [PMID: 33614001 PMCID: PMC7882950 DOI: 10.1002/ece3.7164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 11/26/2020] [Accepted: 12/14/2020] [Indexed: 12/28/2022] Open
Abstract
The maintenance of reproductive isolation in the face of gene flow is a particularly contentious topic, but differences in reproductive behavior may provide the key to explaining this phenomenon. However, we do not yet fully understand how behavior contributes to maintaining species boundaries. How important are behavioral differences during reproduction? To what extent does assortative mating maintain reproductive isolation in recently diverged populations and how important are "magic traits"? Assortative mating can arise as a by-product of accumulated differences between divergent populations as well as an adaptive response to contact between those populations, but this is often overlooked. Here we address these questions using recently described species pairs of three-spined stickleback (Gasterosteus aculeatus), from two separate locations and a phenotypically intermediate allopatric population on the island of North Uist, Scottish Western Isles. We identified stark differences in the preferred nesting substrate and courtship behavior of species pair males. We showed that all males selectively court females of their own ecotype and all females prefer males of the same ecotype, regardless of whether they are from species pairs or allopatric populations. We also showed that mate choice does not appear to be driven by body size differences (a potential "magic trait"). By explicitly comparing the strength of these mating preferences between species pairs and single-ecotype locations, we were able to show that present levels of assortative mating due to direct mate choice are likely a by-product of other adaptations between ecotypes, and not subject to obvious selection in species pairs. Our results suggest that ecological divergence in mating characteristics, particularly nesting microhabitat may be more important than direct mate choice in maintaining reproductive isolation in stickleback species pairs.
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Affiliation(s)
- Laura L. Dean
- School of Life SciencesUniversity of NottinghamNottinghamUK
| | | | - Amelia Reddish
- School of Life SciencesUniversity of NottinghamNottinghamUK
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10
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Ludington AJ, Sanders KL. Demographic analyses of marine and terrestrial snakes (Elapidae) using whole genome sequences. Mol Ecol 2020; 30:545-554. [PMID: 33170980 DOI: 10.1111/mec.15726] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/13/2020] [Accepted: 11/03/2020] [Indexed: 11/27/2022]
Abstract
The question of whether spatial aspects of evolution differ in marine versus terrestrial realms has endured since Ernst Mayr's 1954 essay on marine speciation. Marine systems are often suggested to support larger and more highly connected populations, but quantitative comparisons with terrestrial systems have been lacking. Here, we compared the population histories of marine and terrestrial elapid snakes using the pairwise sequentially Markovian coalescent (PSMC) model to track historical fluctuations in species' effective population sizes (Ne ) from individual whole-genome sequences. To do this we generated a draft genome for the olive sea snake (Aiysurus laevis) and analysed this alongside six published elapid genomes and their sequence reads (marine species Hydrophis curtus, H. melanocephalus and Laticauda laticaudata; terrestrial species Pseudonaja textilis, Naja Naja and Notechis scutatus). Counter to the expectation that marine species should show higher overall Ne and less pronounced fluctuations in Ne , our analyses reveal demographic patterns that are highly variable among species and do not clearly correspond to major ecological divisions. At deeper time intervals, the four marine elapids appear to have experienced relatively stable Ne , while each terrestrial species shows a prominent upturn in Ne starting at ~4 million years ago (Ma) followed by an equally strong decline. However, over the last million years, all seven species show strong and divergent fluctuations. Estimates of Ne in the most recent intervals (~10 kya) are lowest in two of four marine species (H. melanocephalus and Laticauda), and do not correspond to contemporary range sizes in marine or terrestrial taxa.
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Affiliation(s)
- Alastair J Ludington
- School of Biological Science, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kate L Sanders
- School of Biological Science, The University of Adelaide, Adelaide, South Australia, Australia
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11
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Diversity and Distribution of the Dominant Ant Genus Anonychomyrma (Hymenoptera: Formicidae) in the Australian Wet Tropics. DIVERSITY 2020. [DOI: 10.3390/d12120474] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Anonychomyrma is a dolichoderine ant genus of cool-temperate Gondwanan origin with a current distribution that extends from the north of southern Australia into the Australasian tropics. Despite its abundance and ecological dominance, little is known of its species diversity and distribution throughout its range. Here, we describe the diversity and distribution of Anonychomyrma in the Australian Wet Tropics bioregion, where only two of the many putative species are described. We hypothesise that the genus in tropical Australia retains a preference for cool wet rainforests reminiscent of the Gondwanan forests that once dominated Australia, but now only exist in upland habitats of the Wet Tropics. Our study was based on extensive recent surveys across five subregions and along elevation and vertical (arboreal) gradients. We integrated genetic (CO1) data with morphology to recognise 22 species among our samples, 20 of which appeared to be undescribed. As predicted, diversity and endemism were concentrated in uplands above 900 m a.s.l. Distribution modelling of the nine commonest species identified maximum temperature of the warmest month, rainfall seasonality, and rainfall of the wettest month as correlates of distributional patterns across subregions. Our study supported the notion that Anonychomyrma radiated from a southern temperate origin into the tropical zone, with a preference for areas of montane rainforest that were stably cool and wet over the late quaternary.
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12
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Marske KA, Thomaz AT, Knowles LL. Dispersal barriers and opportunities drive multiple levels of phylogeographic concordance in the Southern Alps of New Zealand. Mol Ecol 2020; 29:4665-4679. [PMID: 32991032 DOI: 10.1111/mec.15655] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 08/23/2020] [Accepted: 09/07/2020] [Indexed: 01/23/2023]
Abstract
Phylogeographic concordance, or the sharing of phylogeographic patterns among codistributed species, suggests similar responses to topography or climatic history. While the orientation and timing of breaks between lineages are routinely compared, spatial dynamics within regions occupied by individual lineages provide a second opportunity for comparing responses to past events. In environments with complex topography and glacial history, such as New Zealand's South Island, geographically nested comparisons can identify the processes leading to phylogeographic concordance between and within regional genomic clusters. Here, we used single nucleotide polymorphisms (obtained via ddRADseq) for two codistributed forest beetle species, Agyrtodes labralis (Leiodidae) and Brachynopus scutellaris (Staphylinidae), to evaluate the role of climate change and topography in shaping phylogeographic concordance at two, nested spatial scales: do species diverge over the same geographic barriers, with similar divergence times? And within regions delimited by these breaks, do species share similar spatial dynamics of directional expansion or isolation-by-distance? We found greater congruence of phylogeographic breaks between regions divided by the strongest dispersal barriers (i.e., the Southern Alps). However, these shared breaks were not indicative of shared spatial dynamics within the regions they delimit, and the most similar spatial dynamics between species occurred within regions with the strongest gradients in historical climatic stability. Our results indicate that lack of concordance as traditionally detected by lineage turnover does not rule out the possibility of shared histories, and variation in the presence and type of concordance may provide insights into the different processes shaping phylogeographic patterns across geologically dynamic regions.
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Affiliation(s)
- Katharine A Marske
- Geographical Ecology Group, Department of Biology, University of Oklahoma, Norman, OK, USA.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Andréa T Thomaz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.,Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, BC, Canada.,Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá DC, Colombia
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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13
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Gagnaire PA. Comparative genomics approach to evolutionary process connectivity. Evol Appl 2020; 13:1320-1334. [PMID: 32684961 PMCID: PMC7359831 DOI: 10.1111/eva.12978] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 01/01/2023] Open
Abstract
The influence of species life history traits and historical demography on contemporary connectivity is still poorly understood. However, these factors partly determine the evolutionary responses of species to anthropogenic landscape alterations. Genetic connectivity and its evolutionary outcomes depend on a variety of spatially dependent evolutionary processes, such as population structure, local adaptation, genetic admixture, and speciation. Over the last years, population genomic studies have been interrogating these processes with increasing resolution, revealing a large diversity of species responses to spatially structured landscapes. In parallel, multispecies meta-analyses usually based on low-genome coverage data have provided fundamental insights into the ecological determinants of genetic connectivity, such as the influence of key life history traits on population structure. However, comparative studies still lack a thorough integration of macro- and micro-evolutionary scales to fully realize their potential. Here, I present how a comparative genomics framework may provide a deeper understanding of evolutionary process connectivity. This framework relies on coupling the inference of long-term demographic and selective history with an assessment of the contemporary consequences of genetic connectivity. Standardizing this approach across several species occupying the same landscape should help understand how spatial environmental heterogeneity has shaped the diversity of historical and contemporary connectivity patterns in different taxa with contrasted life history traits. I will argue that a reasonable amount of genome sequence data can be sufficient to resolve and connect complex macro- and micro-evolutionary histories. Ultimately, implementing this framework in varied taxonomic groups is expected to improve scientific guidelines for conservation and management policies.
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14
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Xue AT, Hickerson MJ. Comparative phylogeographic inference with genome‐wide data from aggregated population pairs. Evolution 2020; 74:808-830. [DOI: 10.1111/evo.13945] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/24/2020] [Accepted: 01/29/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Alexander T. Xue
- Subprogram in Ecology, Evolutionary Biology, and Behavior, Department of BiologyGraduate Center of City University of New York New York NY 10016
- Subprogram in Ecology, Evolutionary Biology, and Behavior, Department of BiologyCity College of City University of New York New York NY 10031
- Human Genetics Institute of New Jersey and Department of GeneticsRutgers University Piscataway NJ 08854
- Simons Center for Quantitative BiologyCold Spring Harbor Laboratory Cold Spring Harbor NY 11724
| | - Michael J. Hickerson
- Subprogram in Ecology, Evolutionary Biology, and Behavior, Department of BiologyGraduate Center of City University of New York New York NY 10016
- Subprogram in Ecology, Evolutionary Biology, and Behavior, Department of BiologyCity College of City University of New York New York NY 10031
- Division of Invertebrate ZoologyAmerican Museum of Natural History New York NY 10024
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15
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Yap JS, Merwe M, Ford AJ, Henry RJ, Rossetto M. Biotic exchange leaves detectable genomic patterns in the Australian rain forest flora. Biotropica 2020. [DOI: 10.1111/btp.12776] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jia‐Yee S. Yap
- National Herbarium of New South Wales Royal Botanic Garden Sydney NSW Australia
- Queensland Alliance of Agriculture and Food Innovation University of Queensland Brisbane Qld Australia
| | - Marlien Merwe
- National Herbarium of New South Wales Royal Botanic Garden Sydney NSW Australia
| | - Andrew J. Ford
- CSIRO, Land and Water Tropical Forest Research Centre Atherton Qld Australia
| | - Robert J. Henry
- Queensland Alliance of Agriculture and Food Innovation University of Queensland Brisbane Qld Australia
| | - Maurizio Rossetto
- National Herbarium of New South Wales Royal Botanic Garden Sydney NSW Australia
- Queensland Alliance of Agriculture and Food Innovation University of Queensland Brisbane Qld Australia
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16
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Scalercio S, Cini A, Menchetti M, Vodă R, Bonelli S, Bordoni A, Casacci LP, Dincă V, Balletto E, Vila R, Dapporto L. How long is 3 km for a butterfly? Ecological constraints and functional traits explain high mitochondrial genetic diversity between Sicily and the Italian Peninsula. J Anim Ecol 2020; 89:2013-2026. [PMID: 32207150 DOI: 10.1111/1365-2656.13196] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/21/2020] [Indexed: 11/28/2022]
Abstract
Populations inhabiting Mediterranean islands often show contrasting genetic lineages, even on islands that were connected to the mainland during glacial maxima. This pattern is generated by forces acting in historical and contemporary times. Understanding these phenomena requires comparative studies integrating genetic structure, functional traits and dispersal constraints. Using as a model the butterfly species living across the Messina strait (3 km wide) separating Sicily from the Italian Peninsula, we aimed to unravel the mechanisms limiting the dispersal of matrilines and generating genetic differentiation across a narrow sea strait. We analysed the mitochondrial COI gene of 84 butterfly species out of 90 documented in Sicily and compared them with populations from the neighbouring southern Italian Peninsula (1,398 sequences) and from the entire Palaearctic region (8,093 sequences). For each species, we regressed 13 functional traits and 2 ecological constraints to dispersal (winds experienced at the strait and climatic suitability) against genetic differentiation between Sicily and Italian Peninsula to understand the factors limiting dispersal. More than a third of the species showed different haplogroups across the strait and most of them also represented endemic haplogroups for this island. One fifth of Sicilian populations (and 32.3% of endemic lineages) had their closest relatives in distant areas, instead of the neighbouring Italian Peninsula, which suggests high relictuality. Haplotype diversity was significantly explained by the length of the flight period, an intrinsic phenology trait, while genetic differentiation was explained by both intrinsic traits (wingspan and degree of generalism) and contemporary local constraints (winds experienced at the strait and climatic suitability). A relatively narrow sea strait can produce considerable differentiation among butterfly matrilines and this phenomenon showed a largely deterministic fingerprint. Because of unfavourable winds, populations of the less dispersive Sicilian butterflies tended to differentiate into endemic variants or to maintain relict populations. Understanding these phenomena required the integration of DNA sequences, species traits and physical constraints for a large taxon at continental scale. Future studies may reveal if the patterns here shown for mitochondrial DNA are also reflected in the nuclear genome or, alternatively, are the product of limited female dispersal.
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Affiliation(s)
- Stefano Scalercio
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca Foreste e Legno, Contrada Li Rocchi, Rende, Italy
| | - Alessandro Cini
- Dipartimento di Biologia, Università degli Studi di Firenze, Florence, Italy.,Centre for Biodiversity and Environment Research, University College London, London, UK
| | - Mattia Menchetti
- Dipartimento di Biologia, Università degli Studi di Firenze, Florence, Italy
| | - Raluca Vodă
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Turin, Italy
| | - Simona Bonelli
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Turin, Italy
| | - Adele Bordoni
- Dipartimento di Biologia, Università degli Studi di Firenze, Florence, Italy
| | - Luca Pietro Casacci
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Turin, Italy.,Muzeum i Instytut Zoologii, Polskiej Akademii Nauk, Warsaw, Poland
| | - Vlad Dincă
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Emilio Balletto
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Turin, Italy
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Leonardo Dapporto
- Dipartimento di Biologia, Università degli Studi di Firenze, Florence, Italy
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17
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Gauthier J, de Silva DL, Gompert Z, Whibley A, Houssin C, Le Poul Y, McClure M, Lemaitre C, Legeai F, Mallet J, Elias M. Contrasting genomic and phenotypic outcomes of hybridization between pairs of mimetic butterfly taxa across a suture zone. Mol Ecol 2020; 29:1328-1343. [PMID: 32145112 DOI: 10.1111/mec.15403] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 02/03/2020] [Accepted: 02/21/2020] [Indexed: 11/28/2022]
Abstract
Hybrid zones, whereby divergent lineages come into contact and eventually hybridize, can provide insights on the mechanisms involved in population differentiation and reproductive isolation, and ultimately speciation. Suture zones offer the opportunity to compare these processes across multiple species. In this paper we use reduced-complexity genomic data to compare the genetic and phenotypic structure and hybridization patterns of two mimetic butterfly species, Ithomia salapia and Oleria onega (Nymphalidae: Ithomiini), each consisting of a pair of lineages differentiated for their wing colour pattern and that come into contact in the Andean foothills of Peru. Despite similarities in their life history, we highlight major differences, both at the genomic and phenotypic level, between the two species. These differences include the presence of hybrids, variations in wing phenotype, and genomic patterns of introgression and differentiation. In I. salapia, the two lineages appear to hybridize only rarely, whereas in O. onega the hybrids are not only more common, but also genetically and phenotypically more variable. We also detected loci statistically associated with wing colour pattern variation, but in both species these loci were not over-represented among the candidate barrier loci, suggesting that traits other than wing colour pattern may be important for reproductive isolation. Our results contrast with the genomic patterns observed between hybridizing lineages in the mimetic Heliconius butterflies, and call for a broader investigation into the genomics of speciation in Ithomiini - the largest radiation of mimetic butterflies.
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Affiliation(s)
- Jérémy Gauthier
- Inria, CNRS, IRISA, University Rennes, Rennes, France.,Geneva Natural History Museum, Geneva, Switzerland
| | - Donna Lisa de Silva
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | | | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Céline Houssin
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | - Yann Le Poul
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France.,Fakultat für Biologie, Biozentrum, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Melanie McClure
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | | | | | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Marianne Elias
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
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18
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Patton A, Apodaca JJ, Corser JD, Wilson CR, Williams LA, Cameron AD, Wake DB. A New Green Salamander in the Southern Appalachians: Evolutionary History of Aneides aeneus and Implications for Management and Conservation with the Description of a Cryptic Microendemic Species. COPEIA 2019. [DOI: 10.1643/ch-18-052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Austin Patton
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
| | - Joseph J. Apodaca
- Amphibian and Reptile Conservancy and Tangled Bank Conservation, 128 Bingham Road, Suite 1150, Asheville, North Carolina 28806; . Send reprint requests to this address
| | - Jeffrey D. Corser
- New York Natural Heritage Program, SUNY College of Environmental Science and Forestry, 625 Broadway, 5th Floor, Albany, New York 12233
| | | | - Lori A. Williams
- North Carolina Wildlife Resources Commission, 177 Mountain Laurel Lane, Fletcher, North Carolina 28732
| | - Alan D. Cameron
- North Carolina Wildlife Resources Commission, 177 Mountain Laurel Lane, Fletcher, North Carolina 28732
| | - David B. Wake
- Museum of Vertebrate Zoology, University of California, Berkeley, California 94720-3160
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19
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Dapporto L, Cini A, Vodă R, Dincă V, Wiemers M, Menchetti M, Magini G, Talavera G, Shreeve T, Bonelli S, Casacci LP, Balletto E, Scalercio S, Vila R. Integrating three comprehensive data sets shows that mitochondrial DNA variation is linked to species traits and paleogeographic events in European butterflies. Mol Ecol Resour 2019; 19:1623-1636. [DOI: 10.1111/1755-0998.13059] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 12/16/2022]
Affiliation(s)
| | - Alessandro Cini
- Dipartimento di Biologia dell'Università di Firenze Firenze Italy
- Centre for Biodiversity and Environment Research University College London London UK
| | - Raluca Vodă
- Department of Life Sciences and Systems Biology University of Turin Turin Italy
| | - Vlad Dincă
- Department of Ecology and Genetics University of Oulu Oulu Finland
| | - Martin Wiemers
- Senckenberg Deutsches Entomologisches Institut Müncheberg Germany
- Department of Community Ecology UFZ – Helmholtz Centre for Environmental Research Halle Germany
| | - Mattia Menchetti
- Dipartimento di Biologia dell'Università di Firenze Firenze Italy
- Institut de Biologia Evolutiva (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
| | - Giulia Magini
- Dipartimento di Biologia dell'Università di Firenze Firenze Italy
| | - Gerard Talavera
- Institut de Biologia Evolutiva (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
| | - Tim Shreeve
- Faculty of Health and Life Sciences, Centre for Ecology, Environment and Conservation Oxford Brookes University Oxford UK
| | - Simona Bonelli
- Department of Life Sciences and Systems Biology University of Turin Turin Italy
| | - Luca Pietro Casacci
- Department of Life Sciences and Systems Biology University of Turin Turin Italy
- Museum and Institute of Zoology Polish Academy of Sciences Warsaw Poland
| | - Emilio Balletto
- Department of Life Sciences and Systems Biology University of Turin Turin Italy
| | - Stefano Scalercio
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria Centro di Ricerca Foreste e Legno Rende Italy
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
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20
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Two Divergent Genetic Lineages within the Horned Passalus Beetle, Odontotaenius disjunctus (Coleoptera: Passalidae): An Emerging Model for Insect Behavior, Physiology, and Microbiome Research. INSECTS 2019; 10:insects10060159. [PMID: 31167431 PMCID: PMC6628224 DOI: 10.3390/insects10060159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/24/2019] [Accepted: 05/31/2019] [Indexed: 12/13/2022]
Abstract
The horned passalus (Odontotaenius disjunctus) is one of the most extensively studied saproxylic beetles in the eastern United States. For several decades this species has been the subject of investigations into the behaviors associated with subsociality as well as physiological responses to stress, and, most recently, the composition of its gut microbiome has been closely examined. However, no published study to date has characterized this beetle's broad-scale population genetic structure. Here, we conducted intensive geographic sampling throughout the southern Appalachian Mountains and surrounding areas and then assessed mitochondrial DNA (mtDNA) sequence variation among individuals. Unexpectedly, we discovered two divergent, yet broadly sympatric, mtDNA clades. Indeed, the magnitude of divergence between- vs. within-clades ranged from 5.9 to 7.5×, depending on the dataset under consideration, and members of the two lineages were often syntopic (i.e., found in the same rotting log). Given the potential implications for past and future studies on behavior, physiology, and the gut microbiome, we developed a simple cost-efficient molecular assay (i.e., polymerase chain reaction restriction fragment length polymorphism; PCR-RFLP) to rapidly determine mtDNA clade membership of O. disjunctus individuals. We suggest that the evolutionary processes that gave rise to the emergence and persistence of divergent sympatric lineages reported here warrant investigation, as this type of spatial-genetic pattern appears to be rare among southern Appalachian forest invertebrates.
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21
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Tarnowska E, Niedziałkowska M, Jędrzejewska B. Genetic structure of bank vole populations in the contact zone of two lineages in north-eastern Poland. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2018.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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22
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Evaluating the Hypothesis of Pleistocene Refugia for Mammals in the Cuatro Ciénegas Basin. ANIMAL DIVERSITY AND BIOGEOGRAPHY OF THE CUATRO CIÉNEGAS BASIN 2019. [DOI: 10.1007/978-3-030-11262-2_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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23
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Moran PA, Hunt J, Mitchell C, Ritchie MG, Bailey NW. Behavioural mechanisms of sexual isolation involving multiple modalities and their inheritance. J Evol Biol 2018; 32:243-258. [DOI: 10.1111/jeb.13408] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/15/2018] [Accepted: 11/23/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Peter A. Moran
- School of Biological, Earth and Environmental Sciences University College Cork Cork Ireland
| | - John Hunt
- School of Science and Health Hawkesbury Institute for the Environment Western Sydney University Penrith New South Wales Australia
- Centre for Ecology and Conservation University of Exeter Penryn UK
| | - Christopher Mitchell
- School of Science and Health Hawkesbury Institute for the Environment Western Sydney University Penrith New South Wales Australia
| | - Michael G. Ritchie
- Centre for Biological Diversity School of Biology University of St Andrews Fife UK
| | - Nathan W. Bailey
- Centre for Biological Diversity School of Biology University of St Andrews Fife UK
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24
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Hoffmann AA, Rymer PD, Byrne M, Ruthrof KX, Whinam J, McGeoch M, Bergstrom DM, Guerin GR, Sparrow B, Joseph L, Hill SJ, Andrew NR, Camac J, Bell N, Riegler M, Gardner JL, Williams SE. Impacts of recent climate change on terrestrial flora and fauna: Some emerging Australian examples. AUSTRAL ECOL 2018. [DOI: 10.1111/aec.12674] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ary A. Hoffmann
- Pest and Environmental Adaptation Research Group School of BioSciences Bio21 Institute The University of Melbourne Melbourne Victoria 3010 Australia
| | - Paul D. Rymer
- Hawkesbury Institute for the Environment University of Western Sydney Penrith New South Wales
| | - Margaret Byrne
- Biodiversity and Conservation Science Western Australian Department of Biodiversity, Conservation, and Attractions Science Division Bentley Delivery Centre Bentley Western Australia Australia
| | - Katinka X. Ruthrof
- School of Veterinary and Life Sciences Murdoch University Murdoch Western Australia Australia
- Department of Biodiversity, Conservation and Attractions Kings Park Science Perth Western Australia Australia
| | - Jennie Whinam
- Geography and Spatial Sciences University of Tasmania Hobart Tasmania Australia
| | - Melodie McGeoch
- School of Biological Sciences Monash University Melbourne Victoria Australia
| | | | - Greg R. Guerin
- TERN School of Biological Sciences and Environment Institute University of Adelaide Adelaide South Australia Australia
| | - Ben Sparrow
- TERN School of Biological Sciences and Environment Institute University of Adelaide Adelaide South Australia Australia
| | - Leo Joseph
- Australian National Wildlife Collection National Research Collections Australia CSIRO Canberra Australian Capital Territory Australia
| | - Sarah J. Hill
- Insect Ecology Lab Centre of Excellence for Behavioural and Physiological Ecology University of New England Armidale New South Wales Australia
| | - Nigel R. Andrew
- Insect Ecology Lab Centre of Excellence for Behavioural and Physiological Ecology University of New England Armidale New South Wales Australia
| | - James Camac
- Centre of Excellence for Biosecurity Risk Analysis The University of Melbourne Melbourne Victoria Australia
| | - Nicholas Bell
- Pest and Environmental Adaptation Research Group School of BioSciences Bio21 Institute The University of Melbourne Melbourne Victoria 3010 Australia
| | - Markus Riegler
- Hawkesbury Institute for the Environment University of Western Sydney Penrith New South Wales
| | - Janet L. Gardner
- Division of Ecology & Evolution, Research School of Biology Australian National University Canberra Australian Capital Territory Australia
| | - Stephen E. Williams
- Centre for Tropical Environmental and Sustainability Science College of Science & Engineering James Cook University Townsville Queensland Australia
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25
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Querejeta M, Castresana J. Evolutionary history of the endemic water shrew Neomys anomalus: Recurrent phylogeographic patterns in semi-aquatic mammals of the Iberian Peninsula. Ecol Evol 2018; 8:10138-10146. [PMID: 30397453 PMCID: PMC6206195 DOI: 10.1002/ece3.4487] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/27/2018] [Accepted: 08/08/2018] [Indexed: 11/10/2022] Open
Abstract
The Cabrera's water shrew (Neomys anomalus) is a small semi-aquatic mammal whose taxonomic status was recently elevated from subspecies to species; as a consequence of this change, this species is now endemic to the Iberian Peninsula. In this study, we looked at its evolutionary history by combining phylogeography, the spatial distribution of genetic diversity, and species distribution modeling. To perform these analyses, we used noninvasive samples collected across the species distribution range and sequenced partial mitochondrial cytochrome b and D-loop genes. Maximum-likelihood and Bayesian phylogenetic trees derived from these sequences indicated that N. anomalus is divided into two main phylogroups that correlate strongly with geography, with two contact zones between the groups that showed limited spatial mixing between them. River basins were responsible for only a small percentage of the structure of the genetic diversity of this species despite its riparian habitat. The nucleotide diversity variation map showed the highest genetic diversity to be in the north of the Iberian Peninsula. Finally, species distribution modeling allowed the inference of an optimal area during the Last Interglacial in the north of the Iberian Peninsula, and multiple glacial refugia during the Last Glacial Maximum. The phylogeographic pattern of N. anomalus is strikingly similar to that of another semi-aquatic Iberian mammal, the Pyrenean desman (Galemys pyrenaicus), revealing how Pleistocene glaciations could have had equivalent effects on species of similar ecology and distribution. This phylogeographic structure is consistent with N. anomalus having been isolated for long periods in multiple glacial refugia within the Iberian Peninsula, in agreement with the "refugia-within-refugia" hypothesis, and further supporting its status as a distinct species.
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Affiliation(s)
- Marina Querejeta
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
- Bavarian State Collection of ZoologyMünchenGermany
| | - Jose Castresana
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
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26
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A dated molecular phylogeny of mite harvestmen (Arachnida: Opiliones: Cyphophthalmi) elucidates ancient diversification dynamics in the Australian Wet Tropics. Mol Phylogenet Evol 2018; 127:813-822. [DOI: 10.1016/j.ympev.2018.06.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 06/04/2018] [Accepted: 06/15/2018] [Indexed: 11/20/2022]
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27
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Climatic influences on the genetic structure and distribution of the common vole and field vole in Europe. MAMMAL RES 2018. [DOI: 10.1007/s13364-018-0395-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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28
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Moran PA, Pascoal S, Cezard T, Risse JE, Ritchie MG, Bailey NW. Opposing patterns of intraspecific and interspecific differentiation in sex chromosomes and autosomes. Mol Ecol 2018; 27:3905-3924. [DOI: 10.1111/mec.14725] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 04/13/2018] [Accepted: 04/18/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Peter A. Moran
- School of Biological, Earth and Environmental Sciences; University College Cork; Cork Ireland
| | - Sonia Pascoal
- Department of Zoology; University of Cambridge; Cambridge UK
| | | | - Judith E. Risse
- Bioinformatics; Department of Plant Sciences; Wageningen University; Wageningen The Netherlands
| | - Michael G. Ritchie
- Centre for Biological Diversity; School of Biology; University of St Andrews; St Andrews UK
| | - Nathan W. Bailey
- Centre for Biological Diversity; School of Biology; University of St Andrews; St Andrews UK
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29
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Rodriguero MS, Wirth SA, Alberghina JS, Lanteri AA, Confalonieri VA. A tale of swinger insects: Signatures of past sexuality between divergent lineages of a parthenogenetic weevil revealed by ribosomal intraindividual variation. PLoS One 2018; 13:e0195551. [PMID: 29718921 PMCID: PMC5931498 DOI: 10.1371/journal.pone.0195551] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/23/2018] [Indexed: 12/02/2022] Open
Abstract
Naupactus cervinus (Boheman) (Curculionidae, Naupactini) is a parthenogenetic weevil native to the Paranaense Forest which displays high levels of genetic variation. Two divergent clades were identified, one ranging in forest areas (Forest clade), and the other in open vegetation areas (Grassland clade). Both of them have individuals with high levels of heterozygosity in ribosomal sequences. Investigation of intraindividual variation in ITS1 sequences through cloning and posterior sequencing suggested that mating between both groups most likely occurred in the Paranaense Forest after a secondary contact, which led to fixed heterozygotes as a consequence of parthenogenesis. Otherwise, sexual segregation would have disrupted multilocus genotypes. Only a small number of heterozygous genotypes of all the possible combinations are found in nature. We propose the occurrence of a hybrid zone in the Paranaense Forest. The fact that it is one of the most important biodiversity hotspots of the world, together with its key role for investigating evolutionary processes, makes it worthy of conservation. This is the first genetic evidence of bisexuality in N. cervinus.
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Affiliation(s)
- Marcela S. Rodriguero
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires—IEGEBA (CONICET-UBA), Buenos Aires, Argentina
| | - Sonia A. Wirth
- Laboratorio de Agrobiotecnología, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires e Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA—CONICET/UBA), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Josefina S. Alberghina
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires—IEGEBA (CONICET-UBA), Buenos Aires, Argentina
| | - Analía A. Lanteri
- División Entomología, Museo de La Plata, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata—CONICET, La Plata, Buenos Aires, Argentina
| | - Viviana A. Confalonieri
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires—IEGEBA (CONICET-UBA), Buenos Aires, Argentina
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30
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Singhal S, Hoskin CJ, Couper P, Potter S, Moritz C. A Framework for Resolving Cryptic Species: A Case Study from the Lizards of the Australian Wet Tropics. Syst Biol 2018; 67:1061-1075. [DOI: 10.1093/sysbio/syy026] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/27/2018] [Indexed: 12/19/2022] Open
Affiliation(s)
- Sonal Singhal
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology, California State University—Dominguez Hills, Carson, CA 90747, USA
| | - Conrad J Hoskin
- College of Science & Engineering, James Cook University, Townsville, Queensland 4811, Australia
| | - Patrick Couper
- Biodiversity Program, Queensland Museum, South Brisbane, Queensland 4101, Australia
| | - Sally Potter
- Division of Ecology and Evolution, Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Acton, ACT 2601, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Acton, ACT 2601, Australia
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31
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Bertola LV, Higgie M, Hoskin CJ. Resolving distribution and population fragmentation in two leaf-tailed gecko species of north-east Australia: key steps in the conservation of microendemic species. AUST J ZOOL 2018. [DOI: 10.1071/zo18036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
North Queensland harbours many microendemic species. These species are of conservation concern due to their small and fragmented populations, coupled with threats such as fire and climate change. We aimed to resolve the distribution and population genetic structure in two localised Phyllurus leaf-tailed geckos: P. gulbaru and P. amnicola. We conducted field surveys to better resolve distributions, used Species Distribution Models (SDMs) to assess the potential distribution, and then used the SDMs to target further surveys. We also sequenced all populations for a mitochondrial gene to assess population genetic structure. Our surveys found additional small, isolated populations of both species, including significant range extensions. SDMs revealed the climatic and non-climatic variables that best predict the distribution of these species. Targeted surveys based on the SDMs found P. gulbaru at an additional two sites but failed to find either species at other sites, suggesting that we have broadly resolved their distributions. Genetic analysis revealed population genetic structuring in both species, including deeply divergent mitochondrial lineages. Current and potential threats are overlain on these results to determine conservation listings and identify management actions. More broadly, this study highlights how targeted surveys, SDMs, and genetic data can rapidly increase our knowledge of microendemic species, and direct management.
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32
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Morales-Rozo A, Tenorio EA, Carling MD, Cadena CD. Origin and cross-century dynamics of an avian hybrid zone. BMC Evol Biol 2017; 17:257. [PMID: 29246108 PMCID: PMC5732383 DOI: 10.1186/s12862-017-1096-7] [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] [Received: 04/12/2017] [Accepted: 11/27/2017] [Indexed: 01/07/2023] Open
Abstract
Background Characterizations of the dynamics of hybrid zones in space and time can give insights about traits and processes important in population divergence and speciation. We characterized a hybrid zone between tanagers in the genus Ramphocelus (Aves, Thraupidae) located in southwestern Colombia. We evaluated whether this hybrid zone originated as a result of secondary contact or of primary differentiation, and described its dynamics across time using spatial analyses of molecular, morphological, and coloration data in combination with paleodistribution modeling. Results Models of potential historical distributions based on climatic data and genetic signatures of demographic expansion suggested that the hybrid zone likely originated following secondary contact between populations that expanded their ranges out of isolated areas in the Quaternary. Concordant patterns of variation in phenotypic characters across the hybrid zone and its narrow extent are suggestive of a tension zone, maintained by a balance between dispersal and selection against hybrids. Estimates of phenotypic cline parameters obtained using specimens collected over nearly a century revealed that, in recent decades, the zone appears to have moved to the east and to higher elevations, and may have become narrower. Genetic variation was not clearly structured along the hybrid zone, but comparisons between historical and contemporary specimens suggested that temporal changes in its genetic makeup may also have occurred. Conclusions Our data suggest that the hybrid zone likey resulted from secondary contact between populations. The observed changes in the hybrid zone may be a result of sexual selection, asymmetric gene flow, or environmental change. Electronic supplementary material The online version of this article (doi: 10.1186/s12862-017-1096-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrea Morales-Rozo
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia.,Programa de Biología y Museo de Historia Natural, Universidad de los Llanos, Sede Barcelona, Villavicencio, Colombia
| | - Elkin A Tenorio
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia.,Calima: Fundación para la Investigación de la Biodiversidad y Conservación en el Trópico, Cali, Colombia
| | - Matthew D Carling
- Cornell Laboratory of Ornithology, Cornell University, Ithaca, NY, USA.,Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA
| | - Carlos Daniel Cadena
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia.
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Abstract
Phylogeography and landscape genetics have arisen within the past 30 y. Phylogeography is said to be the bridge between population genetics and systematics, and landscape genetics the bridge between landscape ecology and population genetics. Both fields can be considered as simply the amalgamation of classic biogeography with genetics and genomics; however, they differ in the temporal, spatial, and organismal scales addressed and the methodology used. I begin by briefly summarizing the history and purview of each field and suggest that, even though landscape genetics is a younger field (coined in 2003) than phylogeography (coined in 1987), early studies by Dobzhansky on the "microgeographic races" of Linanthus parryae in the Mojave Desert of California and Drosophila pseudoobscura across the western United States presaged the fields by over 40 y. Recent advances in theory, models, and methods have allowed researchers to better synthesize ecological and evolutionary processes in their quest to answer some of the most basic questions in biology. I highlight a few of these novel studies and emphasize three major areas ripe for investigation using spatially explicit genomic-scale data: the biogeography of speciation, lineage divergence and species delimitation, and understanding adaptation through time and space. Examples of areas in need of study are highlighted, and I end by advocating a union of phylogeography and landscape genetics under the more general field: biogeography.
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Phenotypes in phylogeography: Species' traits, environmental variation, and vertebrate diversification. Proc Natl Acad Sci U S A 2017; 113:8041-8. [PMID: 27432983 DOI: 10.1073/pnas.1602237113] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Almost 30 y ago, the field of intraspecific phylogeography laid the foundation for spatially explicit and genealogically informed studies of population divergence. With new methods and markers, the focus in phylogeography shifted to previously unrecognized geographic genetic variation, thus reducing the attention paid to phenotypic variation in those same diverging lineages. Although phenotypic differences among lineages once provided the main data for studies of evolutionary change, the mechanisms shaping phenotypic differentiation and their integration with intraspecific genetic structure have been underexplored in phylogeographic studies. However, phenotypes are targets of selection and play important roles in species performance, recognition, and diversification. Here, we focus on three questions. First, how can phenotypes elucidate mechanisms underlying concordant or idiosyncratic responses of vertebrate species evolving in shared landscapes? Second, what mechanisms underlie the concordance or discordance of phenotypic and phylogeographic differentiation? Third, how can phylogeography contribute to our understanding of functional phenotypic evolution? We demonstrate that the integration of phenotypic data extends the reach of phylogeography to explain the origin and maintenance of biodiversity. Finally, we stress the importance of natural history collections as sources of high-quality phenotypic data that span temporal and spatial axes.
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Abstract
Phylogeography, and its extensions into comparative phylogeography, have their roots in the layering of gene trees across geography, a paradigm that was greatly facilitated by the nonrecombining, fast evolution provided by animal mtDNA. As phylogeography moves into the era of next-generation sequencing, the specter of reticulation at several levels-within loci and genomes in the form of recombination and across populations and species in the form of introgression-has raised its head with a prominence even greater than glimpsed during the nuclear gene PCR era. Here we explore the theme of reticulation in comparative phylogeography, speciation analysis, and phylogenomics, and ask how the centrality of gene trees has fared in the next-generation era. To frame these issues, we first provide a snapshot of multilocus phylogeographic studies across the Carpentarian Barrier, a prominent biogeographic barrier dividing faunas spanning the monsoon tropics in northern Australia. We find that divergence across this barrier is evident in most species, but is heterogeneous in time and demographic history, often reflecting the taxonomic distinctness of lineages spanning it. We then discuss a variety of forces generating reticulate patterns in phylogeography, including introgression, contact zones, and the potential selection-driven outliers on next-generation molecular markers. We emphasize the continued need for demographic models incorporating reticulation at the level of genomes and populations, and conclude that gene trees, whether explicit or implicit, should continue to play a role in the future of phylogeography.
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Inferring responses to climate dynamics from historical demography in neotropical forest lizards. Proc Natl Acad Sci U S A 2017; 113:7978-85. [PMID: 27432951 DOI: 10.1073/pnas.1601063113] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We apply a comparative framework to test for concerted demographic changes in response to climate shifts in the neotropical lowland forests, learning from the past to inform projections of the future. Using reduced genomic (SNP) data from three lizard species codistributed in Amazonia and the Atlantic Forest (Anolis punctatus, Anolis ortonii, and Polychrus marmoratus), we first reconstruct former population history and test for assemblage-level responses to cycles of moisture transport recently implicated in changes of forest distribution during the Late Quaternary. We find support for population shifts within the time frame of inferred precipitation fluctuations (the last 250,000 y) but detect idiosyncratic responses across species and uniformity of within-species responses across forest regions. These results are incongruent with expectations of concerted population expansion in response to increased rainfall and fail to detect out-of-phase demographic syndromes (expansions vs. contractions) across forest regions. Using reduced genomic data to infer species-specific demographical parameters, we then model the plausible spatial distribution of genetic diversity in the Atlantic Forest into future climates (2080) under a medium carbon emission trajectory. The models forecast very distinct trajectories for the lizard species, reflecting unique estimated population densities and dispersal abilities. Ecological and demographic constraints seemingly lead to distinct and asynchronous responses to climatic regimes in the tropics, even among similarly distributed taxa. Incorporating such constraints is key to improve modeling of the distribution of biodiversity in the past and future.
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Singhal S, Bi K. History cleans up messes: The impact of time in driving divergence and introgression in a tropical suture zone. Evolution 2017; 71:1888-1899. [DOI: 10.1111/evo.13278] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/04/2017] [Indexed: 02/01/2023]
Affiliation(s)
- Sonal Singhal
- Department of Ecology and Evolutionary Biology University of Michigan, 830 North University Ann Arbor Michigan 48109
- Museum of Zoology University of Michigan, 1109 Geddes Avenue Ann Arbor Michigan 48109
| | - Ke Bi
- Museum of Vertebrate Zoology University of California, Berkeley, 3101 Valley Life Sciences Building Berkeley California 94720
- Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences University of California Berkeley California 94720
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Edwards RD, Crisp MD, Cook DH, Cook LG. Congruent biogeographical disjunctions at a continent-wide scale: Quantifying and clarifying the role of biogeographic barriers in the Australian tropics. PLoS One 2017; 12:e0174812. [PMID: 28376094 PMCID: PMC5380322 DOI: 10.1371/journal.pone.0174812] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 03/15/2017] [Indexed: 11/18/2022] Open
Abstract
AIM To test whether novel and previously hypothesized biogeogaphic barriers in the Australian Tropics represent significant disjunction points or hard barriers, or both, to the distribution of plants. LOCATION Australian tropics: Australian Monsoon Tropics and Australian Wet Tropics. METHODS The presence or absence of 6,861 plant species was scored across 13 putative biogeographic barriers in the Australian Tropics, including two that have not previously been recognised. Randomizations of these data were used to test whether more species showed disjunctions (gaps in distribution) or likely barriers (range limits) at these points than expected by chance. RESULTS Two novel disjunctions in the Australian Tropics flora are identified in addition to eleven putative barriers previously recognized for animals. Of these, eleven disjunction points (all within the Australian Monsoon Tropics) were found to correspond to range-ending barriers to a significant number of species, while neither of the two disjunctions found within the Australian Wet Tropics limited a significant number of species' ranges. MAIN CONCLUSIONS Biogeographic barriers present significant distributional limits to native plant species in the Australian Monsoon Tropics but not in the Australian Wet Tropics.
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Affiliation(s)
- Robert D Edwards
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael D Crisp
- Research School of Biology, The Australian National University, Acton, Australian Capital Territory, Australia
| | - Dianne H Cook
- Department of Econometrics and Business Statistics, Monash University, Clayton, Victoria, Australia
| | - Lyn G Cook
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
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Noble C, Laver RJ, Rosauer DF, Ferrier S, Moritz C. Phylogeographic evidence for evolutionary refugia in the Gulf sandstone ranges of northern Australia. AUST J ZOOL 2017. [DOI: 10.1071/zo17079] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Locating and protecting climate change refugia is important to conserving biodiversity with accelerating climate change. Comparative phylogeographic analysis provides an effective tool for locating such refugia, as long-term retention of one or more populations within a refugial landscape will generate unique genetic lineages. The ranges of the western Gulf region of northern Australia are thought to represent a significant arid-zone refugium, in which case low-dispersal organisms should have strong phylogeographic structure across the region. To test for this, we conducted extensive sampling of three species of Gehyra geckos and analysed diversity for mitochondrial DNA and eight nuclear loci. These analyses revealed congruent and high phylogeographic diversity, especially, but not exclusively, in rock-restricted species. This finding, and other recent phylogeographic evidence, demonstrates that these topographically variable landforms have enabled persistence of ecologically diverse vertebrate species through the climate changes of the late Pleistocene. Identification of this relatively under-protected region as a significant climate change refugium points to the need to expand protected areas in this region and to invest in ecological management across existing National Parks and Indigenous Protected Areas.
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40
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Transverse Alpine Speciation Driven by Glaciation. Trends Ecol Evol 2016; 31:916-926. [DOI: 10.1016/j.tree.2016.08.009] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 08/26/2016] [Accepted: 08/26/2016] [Indexed: 01/19/2023]
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41
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Muñoz MM, Langham GM, Brandley MC, Rosauer DF, Williams SE, Moritz C. Basking behavior predicts the evolution of heat tolerance in Australian rainforest lizards. Evolution 2016; 70:2537-2549. [DOI: 10.1111/evo.13064] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 08/15/2016] [Accepted: 08/31/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Martha M. Muñoz
- Department of Biology Duke University Durham North Carolina 27708
| | | | - Matthew C. Brandley
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
| | - Dan F. Rosauer
- Centre for Biodiversity Analysis Australian National University Canberra Australian Capital Territory Australia
- Research School of Biology Australian National University Canberra Australian Capital Territory Australia
| | - Stephen E. Williams
- Centre for Tropical Biodiversity and Climate Change James Cook University Townsville Queensland Australia
| | - Craig Moritz
- Centre for Biodiversity Analysis Australian National University Canberra Australian Capital Territory Australia
- Research School of Biology Australian National University Canberra Australian Capital Territory Australia
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42
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Borowski Z, Świsłocka M, Matosiuk M, Mirski P, Krysiuk K, Czajkowska M, Borkowska A, Ratkiewicz M. Purifying Selection, Density Blocking and Unnoticed Mitochondrial DNA Diversity in the Red Deer, Cervus elaphus. PLoS One 2016; 11:e0163191. [PMID: 27649313 PMCID: PMC5029925 DOI: 10.1371/journal.pone.0163191] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/05/2016] [Indexed: 11/18/2022] Open
Abstract
The trajectories of postglacial range expansions, the occurrence of lineage patches and the formation and maintenance of secondary contact between lineages may mostly reflect neutral demographic processes, including density blocking, that may leave long-lasting genetic signatures. However, a few studies have recently shown that climate may also play a role. We used red deer, a large, mobile herbivore that is assumed to be sensitive to climate change, to test hypotheses of possible selection on the mitochondrial DNA cytochrome b gene (mtDNA cytb) and competitive and/or density-blocking (using mtDNA control region). We searched for a possible link between the phylogeographic structure and abiotic climatic variables. Finally, we tested for isolation by distance and isolation by environment and assessed the impact of human-mediated translocations on the genetic structure of red deer. Our analysis of 30 red deer populations in Poland using the mtDNA control region (N = 357) and cytochrome b (N = 50) markers not only confirmed the presence of the Western and South-Eastern lineages of the species but also indicated the presence of a previously unnoticed, rare relic haplotype that grouped together C. e. italicus from Italy (the Mesola deer). No significant signs of positive selection were detected for the mtDNA cytb gene in the studied red deer. However, a significant signal for purifying selection was found in our study that may explain the narrowness of the contact zone because gene flow between the Western and South-Eastern lineages should drive relatively strong mito-nuclear incompatibilities. MtDNA control region differentiation among red deer populations in Poland correlated with different abiotic climatic variables. Strikingly, the southernmost ice sheet limits during the Elsterian was the most important factor, and it explained the largest amount of variation. However, neither isolation by distance (IBD) nor isolation by environment (IBE) were recorded, and a very limited impact of human translocations was evident. The above-mentioned results suggest that in contemporary red deer populations in Poland, the phylogeographic pattern is well preserved, and long-term processes (density and/or competitive blocking) still play a major role.
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Affiliation(s)
- Zbigniew Borowski
- Department of Forest Ecology, Forest Research Institute, Raszyn, Poland
| | | | - Maciej Matosiuk
- Institute of Biology, University of Bialystok, Bialystok, Poland
| | - Paweł Mirski
- Institute of Biology, University of Bialystok, Bialystok, Poland
| | - Kamil Krysiuk
- Department of Forest Ecology, Forest Research Institute, Raszyn, Poland
| | | | - Anetta Borkowska
- Institute of Biology, University of Bialystok, Bialystok, Poland
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43
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Bryant LM, Krosch MN. Lines in the land: a review of evidence for eastern Australia's major biogeographical barriers to closed forest taxa. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12821] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Litticia M. Bryant
- School of Earth, Environmental and Biological Sciences; Queensland University of Technology; Brisbane Qld 4000 Australia
| | - Matt N. Krosch
- School of Earth, Environmental and Biological Sciences; Queensland University of Technology; Brisbane Qld 4000 Australia
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44
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Robin VV, Vishnudas CK, Gupta P, Ramakrishnan U. Deep and wide valleys drive nested phylogeographic patterns across a montane bird community. Proc Biol Sci 2016; 282:rspb.2015.0861. [PMID: 26085588 DOI: 10.1098/rspb.2015.0861] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Montane species distributions interrupted by valleys can lead to range fragmentation, differentiation and ultimately speciation. Paleoclimatic fluctuations may accentuate or reduce such diversification by temporally altering the extent of montane habitat and may affect species differentially. We examined how an entire montane bird community of the Western Ghats--a linear, coastal tropical mountain range--responds to topographic valleys that host different habitats. Using genetic data from 23 species (356 individuals) collected across nine locations, we examined if different species in the community reveal spatial concordance in population differentiation, and whether the timing of these divergences correlate with climatic events. Our results reveal a nested effect of valleys, with several species (10 of 23) demonstrating the oldest divergences associated with the widest and deepest valley in the mountain range, the Palghat Gap. Further, a subset of these 10 species revealed younger divergences across shallower, narrower valleys. We recovered discordant divergence times for all valley-affected montane birds, mostly in the Pleistocene, supporting the Pliestocene-pump hypotheses and highlighting the role of climatic fluctuations during this period in driving species evolution. A majority of species remain unaffected by valleys, perhaps owing to geneflow or extinction-recolonization dynamics. Studying almost the entire community allowed us to uncover a range of species' responses, including some generalizable and other unpredicted patterns.
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Affiliation(s)
- V V Robin
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India
| | - C K Vishnudas
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India
| | - Pooja Gupta
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, India
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An Ancient Divide in a Contiguous Rainforest: Endemic Earthworms in the Australian Wet Tropics. PLoS One 2015; 10:e0136943. [PMID: 26366862 PMCID: PMC4569478 DOI: 10.1371/journal.pone.0136943] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 08/11/2015] [Indexed: 01/11/2023] Open
Abstract
Understanding the factors that shape current species diversity is a fundamental aim of ecology and evolutionary biology. The Australian Wet Tropics (AWT) are a system in which much is known about how the rainforests and the rainforest-dependent organisms reacted to late Pleistocene climate changes, but less is known about how events deeper in time shaped speciation and extinction in this highly endemic biota. We estimate the phylogeny of a species-rich endemic genus of earthworms (Terrisswalkerius) from the region. Using DEC and DIVA historical biogeography methods we find a strong signal of vicariance among known biogeographical sub-regions across the whole phylogeny, congruent with the phylogeography of less diverse vertebrate groups. Absolute dating estimates, in conjunction with relative ages of major biogeographic disjunctions across Australia, indicate that diversification in Terrisswalkerius dates back before the mid-Miocene shift towards aridification, into the Paleogene era of isolation of mesothermal Gondwanan Australia. For the Queensland endemic Terrisswalkerius earthworms, the AWT have acted as both a museum of biological diversity and as the setting for continuing geographically structured diversification. These results suggest that past events affecting organismal diversification can be concordant across phylogeographic to phylogenetic levels and emphasize the value of multi-scale analysis, from intra- to interspecies, for understanding the broad-scale processes that have shaped geographic diversity.
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46
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Jarnevich CS, Stohlgren TJ, Kumar S, Morisette JT, Holcombe TR. Caveats for correlative species distribution modeling. ECOL INFORM 2015. [DOI: 10.1016/j.ecoinf.2015.06.007] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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47
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Lei F, Qu Y, Song G, Alström P, Fjeldså J. The potential drivers in forming avian biodiversity hotspots in the East Himalaya Mountains of Southwest China. Integr Zool 2015; 10:171-81. [PMID: 25316284 DOI: 10.1111/1749-4877.12121] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Little has been published to describe or interpret Asian biodiversity hotspots, including those in the East Himalayan Mountains of Southwest China (HMSC), thus making necessary a review of the current knowledge. The Pliocene and Pleistocene geological and glacial histories of the Asian continent differ from those of Europe and North America, suggesting different mechanisms of speciation and extinction, and, thus, different responses to climate changes during the Quaternary glaciations. This short review summarizes potential drivers in shaping and maintaining high species richness and endemism of birds in the HMSC. The geographical location at the junction of different biogeographical realms, the wide range of habitats and climates along the extensive elevational range, the complex topography and the distinct geological history of this region have probably contributed to the evolution of an exceptionally species-rich and endemic-rich, specialized montane avian fauna. The Mountain systems in the HMSC may have provided refugia where species survived during the glacial periods and barriers for preventing species dispersal after the glacial periods. More studies are required to further test this refugia hypothesis by comparing more cold-tolerent and warm-tolerent species.
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Affiliation(s)
- Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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48
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Tono A, Iwasaki T, Seo A, Murakami N. Environmental factors contribute to the formation and maintenance of the contact zone observed in deciduous broad-leaved tree species in Japan. JOURNAL OF PLANT RESEARCH 2015; 128:535-551. [PMID: 25850974 DOI: 10.1007/s10265-015-0722-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/25/2015] [Indexed: 06/04/2023]
Abstract
Contact zones are defined as areas where populations from different refugia meet during a postglacial expansion and distinct DNA lineages are mixedly distributed. In Japan, contact zones of various plants and animals were reported from the Kinki-Chugoku region. These contact zones appear to be maintained without any drastic topographic barriers such as those observed in the Alps and Pyrenees Mountains. In this study, the mechanisms underlying the formation and/or maintenance of these contact zones were investigated using six deciduous broad-leaved tree species (Carpinus laxiflora, C. tschonoskii, C. japonica, Magnolia obovata, Padus grayana, and Euonymus oxyphyllus). First, the precise location of the contact zones was examined by intensive genetic analysis of the six species. Second, the relationships between the geographic location of the contact zone and various environmental factors, including climate and topography, were investigated by generalized additive models to reveal the mechanisms of the formation and maintenance of the contact zones. As a result, four of the six examined plant species clearly showed a geographically common contact zone in Hyogo Prefecture and its adjacent areas. The results of the generalized additive models indicate that the pattern of low habitat suitability estimated by ecological niche modeling was the most important factor for determining the location of the common contact zone. These results suggest that areas with low habitat suitability in Hyogo Prefecture restrict the migration and gene flow of the four species in this region, and thus, they maintain the pattern of the contact zones. This study suggests that there are major effects of habitat suitability on the formation and maintenance of the contact zones.
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Affiliation(s)
- Akitaka Tono
- Makino Herbarium, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo, 192-0397, Japan,
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Rosauer DF, Catullo RA, VanDerWal J, Moussalli A, Moritz C. Lineage range estimation method reveals fine-scale endemism linked to Pleistocene stability in Australian rainforest herpetofauna. PLoS One 2015; 10:e0126274. [PMID: 26020936 PMCID: PMC4447262 DOI: 10.1371/journal.pone.0126274] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/31/2015] [Indexed: 12/03/2022] Open
Abstract
Areas of suitable habitat for species and communities have arisen, shifted, and disappeared with Pleistocene climate cycles, and through this shifting landscape, current biodiversity has found paths to the present. Evolutionary refugia, areas of relative habitat stability in this shifting landscape, support persistence of lineages through time, and are thus crucial to the accumulation and maintenance of biodiversity. Areas of endemism are indicative of refugial areas where diversity has persisted, and endemism of intraspecific lineages in particular is strongly associated with late-Pleistocene habitat stability. However, it remains a challenge to consistently estimate the geographic ranges of intraspecific lineages and thus infer phylogeographic endemism, because spatial sampling for genetic analyses is typically sparse relative to species records. We present a novel technique to model the geographic distribution of intraspecific lineages, which is informed by the ecological niche of a species and known locations of its constituent lineages. Our approach allows for the effects of isolation by unsuitable habitat, and captures uncertainty in the extent of lineage ranges. Applying this method to the arc of rainforest areas spanning 3500 km in eastern Australia, we estimated lineage endemism for 53 species of rainforest dependent herpetofauna with available phylogeographic data. We related endemism to the stability of rainforest habitat over the past 120,000 years and identified distinct concentrations of lineage endemism that can be considered putative refugia. These areas of lineage endemism are strongly related to historical stability of rainforest habitat, after controlling for the effects of current environment. In fact, a dynamic stability model that allows movement to track suitable habitat over time was the most important factor in explaining current patterns of endemism. The techniques presented here provide an objective, practical method for estimating geographic ranges below the species level, and including them in spatial analyses of biodiversity.
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Affiliation(s)
- Dan F. Rosauer
- Research School of Biology & Centre for Biodiversity Analysis, Australian National University, Canberra, Australian Capital Territory, Australia
- * E-mail:
| | - Renee A. Catullo
- Research School of Biology & Centre for Biodiversity Analysis, Australian National University, Canberra, Australian Capital Territory, Australia
- CSIRO Land and Water Flagship, Canberra, Australian Capital Territory, Australia
| | - Jeremy VanDerWal
- Centre for Tropical Biodiversity & Climate Change, College of Marine and Environmental Sciences, James Cook University, Townsville, Queensland, Australia
- eResearch Centre, Division of Research and Innovation, James Cook University, Townsville, Queensland, Australia
| | - Adnan Moussalli
- Sciences Department, Museum Victoria, Melbourne, Victoria, Australia
| | - Craig Moritz
- Research School of Biology & Centre for Biodiversity Analysis, Australian National University, Canberra, Australian Capital Territory, Australia
- CSIRO Land and Water Flagship, Canberra, Australian Capital Territory, Australia
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Scott ML, Llewelyn J, Higgie M, Hoskin CJ, Pike K, Phillips BL. Chemoreception and mating behaviour of a tropical Australian skink. Acta Ethol 2015. [DOI: 10.1007/s10211-015-0213-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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