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Pan T, Zhang C, Orozco Terwengel P, Wang H, Ding L, Yang L, Hu C, Li W, Zhou W, Wu X, Zhang B. Comparative phylogeography reveals dissimilar genetic differentiation patterns in two sympatric amphibian species. Integr Zool 2024; 19:863-886. [PMID: 37880913 DOI: 10.1111/1749-4877.12764] [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] [Indexed: 10/27/2023]
Abstract
Global climate change is expected to have a profound effect on species distribution. Due to the temperature constraints, some narrow niche species could shift their narrow range to higher altitudes or latitudes. In this study, we explored the correlation between species traits, genetic structure, and geographical range size. More specifically, we analyzed how these variables are affected by differences in fundamental niche breadth or dispersal ability in the members of two sympatrically distributed stream-dwelling amphibian species (frog, Quasipaa yei; salamander, Pachyhynobius shangchengensis), in Dabie Mountains, East China. Both species showed relatively high genetic diversity in most geographical populations and similar genetic diversity patterns (JTX, low; BYM, high) correlation with habitat changes and population demography. Multiple clustering analyses were used to disclose differentiation among the geographical populations of these two amphibian species. Q. yei disclosed the relatively shallow genetic differentiation, while P. shangchengensis showed an opposite pattern. Under different historical climatic conditions, all ecological niche modeling disclosed a larger suitable habitat area for Q. yei than for P. shangchengensis; these results indicated a wider environment tolerance or wider niche width of Q. yei than P. shangchengensis. Our findings suggest that the synergistic effects of environmental niche variation and dispersal ability may help shape genetic structure across geographical topology, particularly for species with extremely narrow distribution.
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Affiliation(s)
- Tao Pan
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Caiwen Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | | | - Hui Wang
- College of Food and Bioengineering, Bengbu University, Bengbu, China
| | - Ling Ding
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Liuyang Yang
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Chaochao Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Wengang Li
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Wenliang Zhou
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Xiaobing Wu
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Baowei Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
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Dong J, Qiu L, Zhou X, Liu S. Drivers of genomic differentiation landscapes in populations of disparate ecological and geographical settings within mainland Apis cerana. Mol Ecol 2024; 33:e17414. [PMID: 38801184 DOI: 10.1111/mec.17414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024]
Abstract
Elucidating the evolutionary processes that drive population divergence can enhance our understanding of the early stages of speciation and inform conservation management decisions. The honeybee Apis cerana displays extensive population divergence, providing an informative natural system for exploring these processes. The mainland lineage A. cerana includes several peripheral subspecies with disparate ecological and geographical settings radiated from a central ancestor. Under this evolutionary framework, we can explore the patterns of genome differentiation and the evolutionary models that explain them. We can also elucidate the contribution of non-genomic spatiotemporal mechanisms (extrinsic features) and genomic mechanisms (intrinsic features) that influence these genomic differentiation landscapes. Based on 293 whole genomes, a small part of the genome is highly differentiated between central-peripheral subspecies pairs, while low and partial parallelism partly reflects idiosyncratic responses to environmental differences. Combined elements of recurrent selection and speciation-with-gene-flow models generate the heterogeneous genome landscapes. These elements weight differently between central-island and other central-peripheral subspecies pairs, influenced by glacial cycles superimposed on different geomorphologies. Although local recombination rates exert a significant influence on patterns of genomic differentiation, it is unlikely that low-recombination rates regions were generated by structural variation. In conclusion, complex factors including geographical isolation, divergent ecological selection and non-uniform genome features have acted concertedly in the evolution of reproductive barriers that could reduce gene flow in part of the genome and facilitate the persistence of distinct populations within mainland lineage of A. cerana.
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Affiliation(s)
- Jiangxing Dong
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Lifei Qiu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Shanlin Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Wang Z, Wu X, Liu X, Zhang M, Xie C, Chen L. Phylogeographic Structure and Population Dynamics of Baoxing Osmanthus ( Osmanthus serrulatus), an Endemic Species from the Southwest Sichuan Basin, China. PLANTS (BASEL, SWITZERLAND) 2024; 13:1653. [PMID: 38931085 PMCID: PMC11207779 DOI: 10.3390/plants13121653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024]
Abstract
The mountainous regions of southwest China are recognized as pivotal centers for the origin and evolution of Osmanthus species. Baoxing Osmanthus (Osmanthus serrulatus Rehder), a rare and endemic species known for its spring blooms, is sparsely distributed within the high altitude evergreen broad-leaved forests surrounding the southwestern Sichuan Basin. However, persistent anthropogenic disturbances and habitat fragmentation have precipitated a significant decline in its natural population size, leading to the erosion of genetic resources. To assess the genetic status of O. serrulatus and formulate effective conservation strategies, we conducted sampling across ten wild populations, totaling 148 individuals in their natural habitats. We employed two cpDNA fragments (matK and trnS-trnG) to elucidate the phylogeographic structure and historical population dynamics. The results revealed low species-level genetic diversity, alongside pronounced regional differentiation among populations (FST = 0.812, p < 0.05) and a notable phylogeographic structure (NST = 0.698 > GST = 0.396, p < 0.05). Notably, genetic variation was predominantly observed among populations (81.23%), with no evidence of recent demographic expansion across the O. serrulatus distribution range. Furthermore, divergence dating indicated a timeline of approximately 4.85 Mya, corresponding to the late Miocene to early Pleistocene. This temporal correlation coincided with localized uplift events in the southwestern mountains and heightened Asian monsoons, suggesting pivotal roles for these factors in shaping the current phylogeographic pattern of O. serrulatus. These findings support the effective conservation of O. serrulatus germplasm and offer insights into the impact of Quaternary climate oscillations on companion species within evergreen broad-leaved forests. They also enhance our understanding of the origin and evolution of these forests in the southwestern mountains, aiding biodiversity conservation efforts in the region.
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Affiliation(s)
- Zhibei Wang
- Co-Innovation Center for the Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (Z.W.); (X.W.); (X.L.); (M.Z.)
- International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing 210037, China
| | - Xi Wu
- Co-Innovation Center for the Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (Z.W.); (X.W.); (X.L.); (M.Z.)
- International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing 210037, China
| | - Xin Liu
- Co-Innovation Center for the Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (Z.W.); (X.W.); (X.L.); (M.Z.)
- International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing 210037, China
| | - Min Zhang
- Co-Innovation Center for the Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (Z.W.); (X.W.); (X.L.); (M.Z.)
- International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing 210037, China
| | - Chunping Xie
- Tropical Biodiversity and Bioresource Utilization Laboratory, Qiongtai Normal University, Haikou 571127, China;
| | - Lin Chen
- Co-Innovation Center for the Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (Z.W.); (X.W.); (X.L.); (M.Z.)
- International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing 210037, China
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4
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Zhou Y, Tian J, Jiang H, Han M, Wang Y, Lu J. Phylogeography and demographic history of macaques, fascicularis species group, in East Asia: Inferred from multiple genomic markers. Mol Phylogenet Evol 2024; 194:108042. [PMID: 38401812 DOI: 10.1016/j.ympev.2024.108042] [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: 04/30/2023] [Revised: 02/06/2024] [Accepted: 02/18/2024] [Indexed: 02/26/2024]
Abstract
Climate changes at larger scales have influenced dispersal and range shifts of many taxa in East Asia. The fascicularis species group of macaques is composed of four species and is widely distributed in Southeast and East Asia. However, its phylogeography and demographic histories are currently poorly understood. Herein, we assembled autosomal, mitogenome, and Y-chromosome data for 106 individuals, and combined them with 174 mtDNA dloop haplotypes of this species group, with particular focus on the demographic histories and dispersal routes of Macaca fuscata, M. cyclopis, and M. mulatta. The results showed: (1) three monophyletic clades for M. fuscata, M. cyclopis, and M. mulatta based on the multiple genomics analyses; (2) the disparate demographic trajectories of the three species after their split ∼1.0 Ma revealed that M. cyclopis and M. fuscata were derived from an ancestral M. mulatta population; (3) the speciation time of M. cyclopis was later than that of M. fuscata, and their divergence time occurred at the beginning of "Ryukyu Coral Sea Stage" (1.0-0.2 Ma) when the East China Sea land bridge was completely submerged by the sea level rose; and (4) the three parallel rivers (Nujiang, Lancangjiang, and Jinshajiang) of Southwestern China divided M. mulatta into Indian and Chinese genetic populations ∼200 kya. These results shed light on understanding not only the evolutionary history of the fascicularis species group but also the formation mechanism of faunal diversity in East Asia during the Pleistocene.
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Affiliation(s)
- Yanyan Zhou
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou 450001, China
| | - Jundong Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou 450001, China
| | - Haijun Jiang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou 450001, China
| | - Mengya Han
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou 450001, China
| | - Yuwei Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou 450001, China
| | - Jiqi Lu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou 450001, China.
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5
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Shi BY, Pan D, Zhang KQ, Gu TY, Yeo DCJ, Ng PKL, Cumberlidge N, Sun HY. Diversification of freshwater crabs on the sky islands in the Hengduan Mountains Region, China. Mol Phylogenet Evol 2024; 190:107955. [PMID: 37898294 DOI: 10.1016/j.ympev.2023.107955] [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: 07/13/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 10/30/2023]
Abstract
The numerous naturally-fragmented sky islands (SIs) in the Hengduan Mountains Region (HMR) of southwestern China constitute discontinuous landscapes where montane habitats are isolated by dry-hot valleys which have fostered exceptional species diversification and endemicity. However, studies documenting the crucial role of SI on the speciation dynamics of native freshwater organisms are scarce. Here we used a novel set of comprehensive genetic markers (24 nuclear DNA sequences and complete mitogenomes), morphological characters, and biogeographical information to reveal the evolutionary history and speciation mechanisms of a group of small-bodied montane potamids in the genus Tenuipotamon. Our results provide a robustly supported phylogeny, and suggest that the vicariance events of these montane crabs correlate well with the emergence of SIs due to the uplift of the HMR during the Late Oligocene. Furthermore, ancestrally, mountain ridges provided corridors for the dispersal of these montane crabs that led to the colonization of moist montane-specific habitats, aided by past climatic conditions that were the crucial determinants of their evolutionary history. The present results illustrated that the mechanisms isolating SIs are reinforced by the harsh-dry isolating climatic features of dry-hot valleys separating SIs and continue to affect local diversification. This offers insights into the causes of the high biodiversity and endemism shown by the freshwater crabs of the HMR-SIs in southwestern China.
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Affiliation(s)
- Bo-Yang Shi
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Da Pan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
| | - Kang-Qin Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Tian-Yu Gu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Darren C J Yeo
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Republic of Singapore; Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Republic of Singapore
| | - Peter K L Ng
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Republic of Singapore
| | - Neil Cumberlidge
- Department of Biology, Northern Michigan University, Marquette, MI 49855, USA
| | - Hong-Ying Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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6
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Li Z, Linard B, Vogler AP, Yu DW, Wang Z. Phylogenetic diversity only weakly mitigates climate-change-driven biodiversity loss in insect communities. Mol Ecol 2023; 32:6147-6160. [PMID: 36271787 DOI: 10.1111/mec.16747] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 09/28/2022] [Accepted: 10/06/2022] [Indexed: 11/30/2022]
Abstract
To help address the underrepresentation of arthropods and Asian biodiversity from climate-change assessments, we carried out year-long, weekly sampling campaigns with Malaise traps at different elevations and latitudes in Gaoligongshan National Park in southwestern China. From these 623 samples, we barcoded 10,524 beetles and compared scenarios of climate-change-induced biodiversity loss, by designating seasonal, elevational, and latitudinal subsets of beetles as communities that plausibly could go extinct as a group, which we call "loss sets". The availability of a published mitochondrial-genome-based phylogeny of the Coleoptera allowed us to compare the loss of species diversity with and without accounting for phylogenetic relatedness. We hypothesised that phylogenetic relatedness would mitigate extinction, since the extinction of any loss set would result in the disappearance of all its species but only part of its evolutionary history, which is still extant in the remaining loss sets. We found different patterns of community clustering by season and latitude, depending on whether phylogenetic information was incorporated. However, accounting for phylogeny only slightly mitigated the amount of biodiversity loss under climate change scenarios, against our expectations: there is no phylogenetic "escape clause" for biodiversity conservation. We achieve the same results whether phylogenetic information was derived from the mitogenome phylogeny or from a de novo barcode-gene tree. We encourage interested researchers to use this data set to study lineage-specific community assembly patterns in conjunction with life-history traits and environmental covariates.
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Affiliation(s)
- Zongxu Li
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Benjamin Linard
- LIRMM, University of Montpellier, CNRS, Montpellier, France
- SPYGEN, Le Bourget-du-Lac, France
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Zhengyang Wang
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA
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Weng Y, Li H, Yang J, Zhang Z. The past, present, and future of ecogeographic isolation between closely related Aquilegia plants. Ecol Evol 2023; 13:e10098. [PMID: 37250449 PMCID: PMC10212700 DOI: 10.1002/ece3.10098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 03/27/2023] [Accepted: 04/27/2023] [Indexed: 05/31/2023] Open
Abstract
Quantifying the strength of the ecogeographic barrier is an important aspect of plant speciation research, and serves as a practical step to understanding the evolutionary trajectory of plants under climate change. Here, we quantified the extent of ecogeographic isolation in four closely related Aquilegia species that radiated in the Mountains of SW China and adjacent regions, often lacking intrinsic barriers. We used environmental niche models to predict past, present, and future species potential distributions and compared them to determine the degree of overlap and ecogeographic isolation. Our investigation found significant ecological differentiation in all studied species pairs except A. kansuensis and A. ecalacarata. The current strengths of ecogeographic isolation are above 0.5 in most cases. Compared with current climates, most species had an expanding range in the Last Glacial Maximum, the Mid Holocene, and under four future climate scenarios. Our results suggested that ecogeographic isolation contributes to the diversification and maintenance of Aquilegia species in the Mountains of northern and SW China and would act as an essential reproductive barrier in the future.
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Affiliation(s)
- Yulin Weng
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, School of Ecology and Environmental Sciences, Institute of BiodiversityYunnan UniversityKunmingChina
- College of Environment and EcologyXiamen UniversityXiamenChina
| | - Huiqiong Li
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, School of Ecology and Environmental Sciences, Institute of BiodiversityYunnan UniversityKunmingChina
| | - Jiqin Yang
- Gansu Liancheng National Nature ReserveLanzhouChina
| | - Zhi‐Qiang Zhang
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, School of Ecology and Environmental Sciences, Institute of BiodiversityYunnan UniversityKunmingChina
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Wei C, Sangster G, Olsson U, Rasmussen PC, Svensson L, Yao CT, Carey GJ, Leader PJ, Zhang R, Chen G, Song G, Lei F, Wilcove DS, Alström P, Liu Y. Cryptic species in a colorful genus: Integrative taxonomy of the bush robins (Aves, Muscicapidae, Tarsiger) suggests two overlooked species. Mol Phylogenet Evol 2022; 175:107580. [PMID: 35810968 DOI: 10.1016/j.ympev.2022.107580] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/04/2022] [Accepted: 06/16/2022] [Indexed: 10/17/2022]
Abstract
Several cryptic avian species have been validated by recent integrative taxonomic efforts in the Sino-Himalayan mountains, indicating that avian diversity in this global biodiversity hotspot may be underestimated. In the present study, we investigated species limits in the genus Tarsiger, the bush robins, a group of montane forest specialists with high species richness in the Sino-Himalayan region. Based on comprehensive sampling of all 11 subspecies of the six currently recognized species, we applied an integrative taxonomic approach by combining multilocus, acoustic, plumage and morphometric analyses. Our results reveal that the isolated north-central Chinese populations of Tarsiger cyanurus, described as the subspecies albocoeruleus but usually considered invalid, is distinctive in genetics and vocalisation, but only marginally differentiated in morphology. We also found the Taiwan endemic T. indicus formosanus to be distinctive in genetics, song and morphology from T. i. indicus and T. i. yunnanensis of the Sino-Himalayan mountains. Moreover, Bayesian species delimitation using BPP suggests that both albocoeruleus and formosanus merit full species status. We propose their treatment as 'Qilian Bluetail' T. albocoeruleus and 'Taiwan Bush Robin' T. formosanus, respectively.
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Affiliation(s)
- Chentao Wei
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, China; South China Institute of Environmental Sciences, MEE, Guangzhou 510530, China
| | | | - Urban Olsson
- Biology and Environmental Sciences, Systematics and Biodiversity, University of Gothenburg, Box 463, SE-405 30 Göteborg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
| | - Pamela C Rasmussen
- Department of Integrative Biology and MSU Museum, Michigan State University, East Lansing, MI 48864, USA; Bird Group, The Natural History Museum-UK, Akeman Street, Tring, UK
| | | | - Cheng-Te Yao
- Medium Altitude Experimental Station, Endemic Species Research Institute, Chichi, 15 Nantou 552, Taiwan, China
| | - Geoff J Carey
- AEC Ltd, 127 Commercial Centre, Palm Springs, Hong Kong, China
| | - Paul J Leader
- AEC Ltd, 127 Commercial Centre, Palm Springs, Hong Kong, China
| | - Ruiying Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guoling Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - David S Wilcove
- Princeton School of Public and International Affairs, Princeton University, NJ 08544, USA; Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, China.
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9
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Wang Z, Pierce NE. Fine-scale genome-wide signature of Pleistocene glaciation in Thitarodes moths (Lepidoptera: Hepialidae), host of Ophiocordyceps fungus in the Hengduan Mountains. Mol Ecol 2022; 32:2695-2714. [PMID: 35377501 DOI: 10.1111/mec.16457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 02/12/2022] [Accepted: 03/21/2022] [Indexed: 11/28/2022]
Abstract
The Hengduan Mountains region is a biodiversity hotspot known for its topologically complex, deep valleys and high mountains. While landscape and glacial refugia have been evoked to explain patterns of inter-species divergence, the accumulation of intra-species (i.e. population level) genetic divergence across the mountain-valley landscape in this region has received less attention. We used genome-wide restriction site-associated DNA sequencing (RADseq) to reveal signatures of Pleistocene glaciation in populations of Thitarodes shambalaensis (Lepidoptera: Hepialidae), the host moth of parasitic Ophiocordyceps sinensis (Hypocreales: Ophiocordycipitaceae) or "caterpillar fungus" endemic to the glacier of eastern Mt. Gongga. We used moraine history along the glacier valleys to model the distribution and environmental barriers to gene flow across populations of T. shambalaensis. We found that moth populations separated by less than 10 km exhibited valley-based population genetic clustering and isolation-by-distance (IBD), while gene flow among populations was best explained by models using information about their distributions at the local last glacial maximum (LGML , 58 kya), not their contemporary distribution. Maximum likelihood lineage history among populations, and among subpopulations as little as 500 meters apart, recapitulated glaciation history across the landscape. We also found signals of isolated population expansion following the retreat of LGML glaciers. These results reveal the fine-scale, long-term historical influence of landscape and glaciation on the genetic structuring of populations of an endangered and economically important insect species. Similar mechanisms, given enough time and continued isolation, could explain the contribution of glacier refugia to the generation of species diversity among the Hengduan Mountains.
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Affiliation(s)
- Zhengyang Wang
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Naomi E Pierce
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
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10
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Wang X, Tong L, Deng J, Li L, Xiang P, Xu L, Luo Z, Yang K, Song Z. Insights into historical drainage evolution based on the phylogeography of Schizopygopsis malacanthus Herzenstein (Cypriniformes, Cyprinidae) across the upper and middle Yalong River drainage in the Hengduan Mountains region, southwest China. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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11
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Integrating Earth–life systems: a geogenomic approach. Trends Ecol Evol 2022; 37:371-384. [DOI: 10.1016/j.tree.2021.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/04/2021] [Accepted: 12/08/2021] [Indexed: 12/26/2022]
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Dolby GA. Towards a unified framework to study causality in Earth-life systems. Mol Ecol 2021; 30:5628-5642. [PMID: 34427004 PMCID: PMC9292314 DOI: 10.1111/mec.16142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 07/17/2021] [Accepted: 08/20/2021] [Indexed: 01/04/2023]
Abstract
There is considerable interest in better understanding how earth processes shape the generation and distribution of life on Earth. This question, at its heart, is one of causation. In this article I propose that at a regional level, earth processes can be thought of as behaving somewhat deterministically and may have an organized effect on the diversification and distribution of species. However, the study of how landscape features shape biology is challenged by pseudocongruent or collinear variables. I demonstrate that causal structures can be used to depict the cause–effect relationships between earth processes and biological patterns using recent examples from the literature about speciation and species richness in montane settings. This application shows that causal diagrams can be used to better decipher the details of causal relationships by motivating new hypotheses. Additionally, the abstraction of this knowledge into structural equation metamodels can be used to formulate theory about relationships within Earth–life systems more broadly. Causal structures are a natural point of collaboration between biologists and Earth scientists, and their use can mitigate against the risk of misassigning causality within studies. My goal is that by applying causal theory through application of causal structures, we can build a systems‐level understanding of what landscape features or earth processes most shape the distribution and diversification of species, what types of organisms are most affected, and why.
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Affiliation(s)
- Greer A Dolby
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA.,Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
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Walton W, Stone GN, Lohse K. Discordant Pleistocene population size histories in a guild of hymenopteran parasitoids. Mol Ecol 2021; 30:4538-4550. [PMID: 34252238 DOI: 10.1111/mec.16074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 06/23/2021] [Accepted: 07/06/2021] [Indexed: 01/03/2023]
Abstract
Signatures of past changes in population size have been detected in genome-wide variation in many species. However, the causes of such demographic changes and the extent to which they are shared across co-distributed species remain poorly understood. During Pleistocene glacial maxima, many temperate European species were confined to southern refugia. While vicariance and range expansion processes associated with glacial cycles have been widely documented, it is unclear whether refugial populations of co-distributed species have experienced shared histories of population size change. We analyse whole-genome sequence data to reconstruct and compare demographic histories during the Quaternary for Iberian refuge populations in a single ecological guild (seven species of chalcid parasitoid wasps associated with oak cynipid galls). For four of these species, we find support for large changes in effective population size (Ne ) through the Pleistocene that coincide with major climate events. However, there is little evidence that the timing, direction and magnitude of demographic change are shared across species, suggesting that demographic histories in this guild are largely idiosyncratic, even at the scale of a single glacial refugium.
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Affiliation(s)
- William Walton
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Graham N Stone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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Wan T, Oaks JR, Jiang XL, Huang H, Knowles LL. Differences in Quaternary co-divergence reveals community-wide diversification in the mountains of southwest China varied among species. Proc Biol Sci 2021; 288:20202567. [PMID: 33402075 DOI: 10.1098/rspb.2020.2567] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The mountains of southwest China (MSWC) is a biodiversity hotspot with highly complex and unusual terrain. However, with the majority of studies focusing on the biogeographic consequences of massive mountain building, the Quaternary legacy of biodiversity for the MSWC has long been overlooked. Here, we took a statistical comparative phylogeography approach to examine factors that shaped community-wide diversification. With data from 30 vertebrate species, the results reveal spatially concordant genetic structure, and temporally clustered co-divergence events associated with river barriers during severe glacial cycles. This indicates the importance of riverine barriers in the phylogeographic history of the MSWC vertebrate community. We conclude that the repeated glacial cycles are associated with co-divergences that are themselves structured by the heterogeneity of the montane landscape of the MSWC. This orderly process of diversification has profound implications for conservation by highlighting the relative independence of different geographical areas in which some, but not all species in communities have responded similarly to climate change and calls for further comparative phylogeographic investigations to reveal the connection between biological traits and divergence pulses in this biodiversity hotspot.
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Affiliation(s)
- Tao Wan
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, People's Republic of China.,Mammal Ecology and Evolution, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People's Republic of China.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.,College of Life Sciences, Sichuan Normal University, Chengdu 610066, People's Republic of China
| | - Jamie R Oaks
- Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | - Xue-Long Jiang
- Mammal Ecology and Evolution, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People's Republic of China
| | - Huateng Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, People's Republic of China
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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