1
|
Shi W, Maqsood I, Liu K, Yu M, Si Y, Rong K. Community Diversity of Fungi Carried by Four Common Woodpeckers in Heilongjiang Province, China. J Fungi (Basel) 2024; 10:389. [PMID: 38921375 PMCID: PMC11204829 DOI: 10.3390/jof10060389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024] Open
Abstract
Woodpeckers exhibit selectivity when choosing tree cavities for nest development in forest ecosystems, and fungi play a significant and important role in this ecological process. Therefore, there is a complex and intricate relationship between the various behaviors of woodpeckers and the occurrence of fungal species. Research into the complex bond between fungi and woodpeckers was undertaken to provide more information about this remarkable ecological relationship. Through the process of line transect sampling, woodpecker traces were searched for, and mist nets were set up to capture them. A total of 21 woodpeckers belonging to four species were captured. High-throughput sequencing of the ITS region was performed on fungal-conserved samples to enable an in-depth analysis of the fungal communities linked to the woodpeckers' nests. Members of Ascomycota were the most abundant in the samples, accounting for 91.96% of the total, demonstrating the importance of this group in the forest ecosystem of this station. The statistical results indicate significant differences in the fungal diversity carried by woodpeckers among the different groups. Species of Cladosporium were found to be the most prevalent of all the detected fungal genera, accounting for 49.3%. The top 15 most abundant genera were Cladosporium, Trichoderma, Beauveria, Epicococcum, Hypoxylon, Penicillium, Nigrospora, Aspergillus, Oidiodendron, Cercospora, Talaromyces, Phialemo-nium, Petriella, Cordyceps, and Sistotrema. The standard Bray-Curtis statistical technique was used in a hierarchical clustering analysis to compute inter-sample distances, allowing for the identification of patterns and correlations within the dataset. We discovered that in the grouped samples from woodpeckers, there were differences in the diversity of fungal communities carried by four woodpecker species, but the less dominant fungal species were still similar. The findings highlight the need to consider these diverse ecological linkages in woodpecker research and conservation efforts.
Collapse
Affiliation(s)
- Wenhui Shi
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Iram Maqsood
- Department of Zoology, Shaheed Benazir Bhutto Women University Peshawar Pakistan, Peshawar 25000, Pakistan
| | - Keying Liu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Meichen Yu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Yuhui Si
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Ke Rong
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Wildlife Conservation Biology, National Forestry and Grassland Administration, Beijing 100013, China
| |
Collapse
|
2
|
Daniel A, Savary P, Foltête JC, Khimoun A, Faivre B, Ollivier A, Éraud C, Moal H, Vuidel G, Garnier S. Validating graph-based connectivity models with independent presence-absence and genetic data sets. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023; 37:e14047. [PMID: 36661070 DOI: 10.1111/cobi.14047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/11/2022] [Accepted: 11/22/2022] [Indexed: 05/11/2023]
Abstract
Habitat connectivity is a key objective of current conservation policies and is commonly modeled by landscape graphs (i.e., sets of habitat patches [nodes] connected by potential dispersal paths [links]). These graphs are often built based on expert opinion or species distribution models (SDMs) and therefore lack empirical validation from data more closely reflecting functional connectivity. Accordingly, we tested whether landscape graphs reflect how habitat connectivity influences gene flow, which is one of the main ecoevolutionary processes. To that purpose, we modeled the habitat network of a forest bird (plumbeous warbler [Setophaga plumbea]) on Guadeloupe with graphs based on expert opinion, Jacobs' specialization indices, and an SDM. We used genetic data (712 birds from 27 populations) to compute local genetic indices and pairwise genetic distances. Finally, we assessed the relationships between genetic distances or indices and cost distances or connectivity metrics with maximum-likelihood population-effects distance models and Spearman correlations between metrics. Overall, the landscape graphs reliably reflected the influence of connectivity on population genetic structure; validation R2 was up to 0.30 and correlation coefficients were up to 0.71. Yet, the relationship among graph ecological relevance, data requirements, and construction and analysis methods was not straightforward because the graph based on the most complex construction method (species distribution modeling) sometimes had less ecological relevance than the others. Cross-validation methods and sensitivity analyzes allowed us to make the advantages and limitations of each construction method spatially explicit. We confirmed the relevance of landscape graphs for conservation modeling but recommend a case-specific consideration of the cost-effectiveness of their construction methods. We hope the replication of independent validation approaches across species and landscapes will strengthen the ecological relevance of connectivity models.
Collapse
Affiliation(s)
- Alexandrine Daniel
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, Dijon, France
| | - Paul Savary
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, Dijon, France
- ThéMA, UMR 6049 CNRS, Université de Franche-Comté, Besançon, France
- ARP-Astrance, Paris, France
| | | | - Aurélie Khimoun
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, Dijon, France
| | - Bruno Faivre
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, Dijon, France
| | - Anthony Ollivier
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, Dijon, France
| | - Cyril Éraud
- Office Français de la Biodiversité, Chizé, France
| | | | - Gilles Vuidel
- ThéMA, UMR 6049 CNRS, Université de Franche-Comté, Besançon, France
| | - Stéphane Garnier
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, Dijon, France
| |
Collapse
|
3
|
Genetic diversity and spatial genetic structure support the specialist-generalist variation hypothesis in two sympatric woodpecker species. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01451-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractSpecies are often arranged along a continuum from “specialists” to “generalists”. Specialists typically use fewer resources, occur in more patchily distributed habitats and have overall smaller population sizes than generalists. Accordingly, the specialist-generalist variation hypothesis (SGVH) proposes that populations of habitat specialists have lower genetic diversity and are genetically more differentiated due to reduced gene flow compared to populations of generalists. Here, expectations of the SGVH were tested by examining genetic diversity, spatial genetic structure and contemporary gene flow in two sympatric woodpecker species differing in habitat specialization. Compared to the generalist great spotted woodpecker (Dendrocopos major), lower genetic diversity was found in the specialist middle spotted woodpecker (Dendrocoptes medius). Evidence for recent bottlenecks was revealed in some populations of the middle spotted woodpecker, but in none of the great spotted woodpecker. Substantial spatial genetic structure and a significant correlation between genetic and geographic distances were found in the middle spotted woodpecker, but only weak spatial genetic structure and no significant correlation between genetic and geographic distances in the great spotted woodpecker. Finally, estimated levels of contemporary gene flow did not differ between the two species. Results are consistent with all but one expectations of the SGVH. This study adds to the relatively few investigations addressing the SGVH in terrestrial vertebrates.
Collapse
|
4
|
Pavlova A, Harrisson KA, Turakulov R, Lee YP, Ingram BA, Gilligan D, Sunnucks P, Gan HM. Labile sex chromosomes in the Australian freshwater fish family Percichthyidae. Mol Ecol Resour 2021; 22:1639-1655. [PMID: 34863023 DOI: 10.1111/1755-0998.13569] [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: 02/09/2021] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 12/01/2022]
Abstract
Sex-specific ecology has management implications, but rapid sex-chromosome turnover in fishes hinders sex-marker development for monomorphic species. We used annotated genomes and reduced-representation sequencing data for two Australian percichthyids, Macquarie perch Macquaria australasica and golden perch M. ambigua, and whole genome resequencing for 50 Macquarie perch of each sex, to identify sex-linked loci and develop an affordable sexing assay. In silico pool-seq tests of 1,492,004 Macquarie perch SNPs revealed that a 275-kb scaffold was enriched for gametologous loci. Within this scaffold, 22 loci were sex-linked in a predominantly XY system, with females being homozygous for the X-linked allele at all 22, and males having the Y-linked allele at >7. Seven XY-gametologous loci (all males, but no females, are heterozygous or homozygous for the male-specific allele) were within a 146-bp region. A PCR-RFLP sexing assay targeting one Y-linked SNP, tested in 66 known-sex Macquarie perch and two of each sex of three confamilial species, plus amplicon sequencing of 400 bp encompassing the 146-bp region, revealed that the few sex-linked positions differ between species and between Macquarie perch populations. This indicates sex-chromosome lability in Percichthyidae, supported by nonhomologous scaffolds containing sex-linked loci for Macquarie- and golden perches. The present resources facilitate genomic research in Percichthyidae, including formulation of hypotheses about candidate genes of interest such as transcription factor SOX1b that occurs in the 275-kb scaffold ~38 kb downstream of the 146-bp region containing seven XY-gametologous loci. Sex-linked markers will be useful for determining genetic sex in some populations and studying sex chromosome turnover.
Collapse
Affiliation(s)
- Alexandra Pavlova
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Katherine A Harrisson
- Department of Ecology, Environment & Evolution, La Trobe University, Bundoora, Vic., Australia.,Department of Environment, Land, Water and Planning, Arthur Rylah Institute for Environmental Research, Heidelberg, Vic., Australia
| | - Rustam Turakulov
- Division of Ecology and Evolution, RSB, Australian National University, Acton, ACT, Australia
| | - Yin Peng Lee
- School of Life and Environmental Sciences, Deakin University, Geelong, Vic., Australia.,Deakin Genomics Centre, Deakin University, Geelong, Vic., Australia
| | | | - Dean Gilligan
- Freshwater Ecosystems Research, New South Wales Department of Primary Industries - Fisheries, Batemans Bay, NSW, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Han Ming Gan
- School of Life and Environmental Sciences, Deakin University, Geelong, Vic., Australia.,Deakin Genomics Centre, Deakin University, Geelong, Vic., Australia.,GeneSEQ Sdn Bhd, Rawang, Malaysia
| |
Collapse
|
5
|
Mulvaney JM, Matthee CA, Cherry MI. Species-landscape interactions drive divergent population trajectories in four forest-dependent Afromontane forest songbird species within a biodiversity hotspot in South Africa. Evol Appl 2021; 14:2680-2697. [PMID: 34815747 PMCID: PMC8591328 DOI: 10.1111/eva.13306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/19/2021] [Accepted: 09/26/2021] [Indexed: 11/27/2022] Open
Abstract
Species confined to naturally fragmented habitats may exhibit intrinsic population complexity which may challenge interpretations of species response to anthropogenic landscape transformation. In South Africa, where native forests are naturally fragmented, forest-dependent birds have undergone range declines since 1992, most notably among insectivores. These insectivores appear sensitive to the quality of natural matrix habitats, and it is unknown whether transformation of the landscape matrix has disrupted gene flow in these species. We undertook a landscape genetics study of four forest-dependent insectivorous songbirds across southeast South Africa. Microsatellite data were used to conduct a priori optimization of landscape resistance surfaces (land cover, rivers and dams, and elevation) using cost-distances along least-cost pathway (LCP), and resistance distances (IBR). We detected pronounced declines in effective population sizes over the past two centuries for the endemic forest specialist Cossypha dichroa and Batis capensis, alongside recent gene flow disruption in B. capensis, C. dichroa and Pogonocichla stellata. Landscape resistance modelling showed both native forest and dense thicket configuration facilitates gene flow in P. stellata, B. capensis and C. dichroa. Facultative dispersal of P. stellata through dense thicket likely aided resilience against historic landscape transformation, whereas combined forest-thicket degradation adversely affected the forest generalist B. capensis. By contrast, Phylloscopus ruficapilla appears least reliant upon landscape features to maintain gene flow and was least impacted by anthropogenic landscape transformation. Collectively, gene flow in all four species is improved at lower elevations, along river valleys, and riparian corridors- where native forest and dense thicket better persist. Consistent outperformance of LCP over IBR land-cover models for P. stellata, B. capensis and C. dichroa demonstrates the benefits of wildlife corridors for South African forest-dependent bird conservation, to ameliorate the extinction debts from past and present anthropogenic forest exploitation.
Collapse
Affiliation(s)
- Jake M. Mulvaney
- Department of Botany and ZoologyStellenbosch UniversityMatielandSouth Africa
| | - Conrad A. Matthee
- Department of Botany and ZoologyStellenbosch UniversityMatielandSouth Africa
| | - Michael I. Cherry
- Department of Botany and ZoologyStellenbosch UniversityMatielandSouth Africa
| |
Collapse
|
6
|
Rönkä N, Pakanen VM, Pauliny A, Thomson RL, Nuotio K, Pehlak H, Thorup O, Lehikoinen P, Rönkä A, Blomqvist D, Koivula K, Kvist L. Genetic differentiation in an endangered and strongly philopatric, migrant shorebird. BMC Ecol Evol 2021; 21:125. [PMID: 34147062 PMCID: PMC8214799 DOI: 10.1186/s12862-021-01855-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/08/2021] [Indexed: 11/24/2022] Open
Abstract
Background Populations living in fragmented habitats may suffer from loss of genetic variation and reduced between-patch dispersal, which are processes that can result in genetic differentiation. This occurs frequently in species with reduced mobility, whereas genetic differentiation is less common among mobile species such as migratory birds. The high dispersal capacity in the latter species usually allows for gene flow even in fragmented landscapes. However, strongly philopatric behaviour can reinforce relative isolation and the degree of genetic differentiation. The Southern Dunlin (Calidris alpina schinzii) is a philopatric, long-distance migratory shorebird and shows reduced dispersal between isolated breeding patches. The endangered population of the Southern Dunlin breeding at the Baltic Sea has suffered from habitat deterioration and fragmentation of coastal meadows. We sampled DNA across the entire population and used 12 polymorphic microsatellite loci to examine whether the environmental changes have resulted in genetic structuring and loss of variation. Results We found a pattern of isolation-by-distance across the whole Baltic population and genetic differentiation between local populations, even within the southern Baltic. Observed heterozygosity was lower than expected throughout the range and internal relatedness values were positive indicating inbreeding. Conclusions Our results provide long-term, empirical evidence for the theoretically expected links between habitat fragmentation, population subdivision, and gene flow. They also demonstrate a rare case of genetic differentiation between populations of a long-distance migratory species. The Baltic Southern Dunlin differs from many related shorebird species that show near panmixia, reflecting its philopatric life history and the reduced connectivity of its breeding patches. The results have important implications as they suggest that reduced connectivity of breeding habitats can threaten even long-distance migrants if they show strong philopatry during breeding. The Baltic Southern Dunlin warrants urgent conservation efforts that increase functional connectivity and gene flow between breeding areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01855-0.
Collapse
Affiliation(s)
- Nelli Rönkä
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
| | - Veli-Matti Pakanen
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland.,Department of Biological and Environmental Sciences, University of Gothenburg, P.O. Box 463, 405 30, Gothenburg, Sweden
| | - Angela Pauliny
- Department of Biological and Environmental Sciences, University of Gothenburg, P.O. Box 463, 405 30, Gothenburg, Sweden
| | - Robert L Thomson
- Section of Ecology, Department of Biology, University of Turku, 20014, Turku, Finland.,Percy FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch, 7701, South Africa
| | - Kimmo Nuotio
- Environmental Agency, Valtakatu 11, 28100, Pori, Finland
| | - Hannes Pehlak
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, 51014, Tartu, Estonia.,OÜ Xenus, Koguva, 94724, Muhu Island, Saare, Estonia
| | - Ole Thorup
- , V. Vedsted Byvej 32, Vester Vedsted, 6760, Ribe, Denmark
| | - Petteri Lehikoinen
- The Helsinki Lab of Ornithology, Finnish Museum of Natural History, University of Helsinki, 00014, Helsinki, Finland
| | - Antti Rönkä
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
| | - Donald Blomqvist
- Department of Biological and Environmental Sciences, University of Gothenburg, P.O. Box 463, 405 30, Gothenburg, Sweden.
| | - Kari Koivula
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
| | - Laura Kvist
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
| |
Collapse
|
7
|
Kudla N, McCluskey EM, Lulla V, Grundel R, Moore JA. Intact landscape promotes gene flow and low genetic structuring in the threatened Eastern Massasauga Rattlesnake. Ecol Evol 2021; 11:6276-6288. [PMID: 34141217 PMCID: PMC8207425 DOI: 10.1002/ece3.7480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/07/2020] [Accepted: 02/01/2021] [Indexed: 11/07/2022] Open
Abstract
Genetic structuring of wild populations is dependent on environmental, ecological, and life-history factors. The specific role environmental context plays in genetic structuring is important to conservation practitioners working with rare species across areas with varying degrees of fragmentation. We investigated fine-scale genetic patterns of the federally threatened Eastern Massasauga Rattlesnake (Sistrurus catenatus) on a relatively undisturbed island in northern Michigan, USA. This species often persists in habitat islands throughout much of its distribution due to extensive habitat loss and distance-limited dispersal. We found that the entire island population exhibited weak genetic structuring with spatially segregated variation in effective migration and genetic diversity. The low level of genetic structuring contrasts with previous studies in the southern part of the species' range at comparable fine scales (~7 km), in which much higher levels of structuring were documented. The island population's genetic structuring more closely resembles that of populations from Ontario, Canada, that occupy similarly intact habitats. Intrapopulation variation in effective migration and genetic diversity likely corresponds to the presence of large inland lakes acting as barriers and more human activity in the southern portion of the island. The observed genetic structuring in this intact landscape suggests that the Eastern Massasauga is capable of sufficient interpatch movements to reduce overall genetic structuring and colonize new habitats. Landscape mosaics with multiple habitat patches and localized barriers (e.g., large water bodies or roads) will promote gene flow and natural colonization for this declining species.
Collapse
Affiliation(s)
- Nathan Kudla
- Biology DepartmentGrand Valley State UniversityAllendaleMIUSA
| | | | - Vijay Lulla
- Department of GeographyIUPUIIndianapolis, INUSA
| | - Ralph Grundel
- Great Lakes Science CenterU.S. Geological SurveyChestertonINUSA
| | | |
Collapse
|
8
|
Isolation-by-distance and male-biased dispersal at a fine spatial scale: a study of the common European adder (Vipera berus) in a rural landscape. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01365-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
9
|
García NC, Robinson WD. Current and Forthcoming Approaches for Benchmarking Genetic and Genomic Diversity. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.622603] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The current attrition of biodiversity extends beyond loss of species and unique populations to steady loss of a vast genomic diversity that remains largely undescribed. Yet the accelerating development of new techniques allows us to survey entire genomes ever faster and cheaper, to obtain robust samples from a diversity of sources including degraded DNA and residual DNA in the environment, and to address conservation efforts in new and innovative ways. Here we review recent studies that highlight the importance of carefully considering where to prioritize collection of genetic samples (e.g., organisms in rapidly changing landscapes or along edges of geographic ranges) and what samples to collect and archive (e.g., from individuals of little-known subspecies or populations, even of species not currently considered endangered). Those decisions will provide the sample infrastructure to detect the disappearance of certain genotypes or gene complexes, increases in inbreeding levels, and loss of genomic diversity as environmental conditions change. Obtaining samples from currently endangered, protected, and rare species can be particularly difficult, thus we also focus on studies that use new, non-invasive ways of obtaining genomic samples and analyzing them in these cases where other sampling options are highly constrained. Finally, biological collections archiving such samples face an inherent contradiction: their main goal is to preserve biological material in good shape so it can be used for scientific research for centuries to come, yet the technologies that can make use of such materials are advancing faster than collections can change their standardized practices. Thus, we also discuss current and potential new practices in biological collections that might bolster their usefulness for future biodiversity conservation research.
Collapse
|
10
|
Dudaniec RY, Carey AR, Svensson EI, Hansson B, Yong CJ, Lancaster LT. Latitudinal clines in sexual selection, sexual size dimorphism and sex-specific genetic dispersal during a poleward range expansion. J Anim Ecol 2021; 91:1104-1118. [PMID: 33759189 DOI: 10.1111/1365-2656.13488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 03/09/2021] [Indexed: 10/21/2022]
Abstract
Range expansions can be shaped by sex differences in behaviours and other phenotypic traits affecting dispersal and reproduction. Here, we investigate sex differences in morphology, behaviour and genomic population differentiation along a climate-mediated range expansion in the common bluetail damselfly (Ischnura elegans) in northern Europe. We sampled 65 sites along a 583-km gradient spanning the I. elegans range in Sweden and quantified latitudinal gradients in site relative abundance, sex ratio and sex-specific shifts in body size and mating status (a measure of sexual selection). Using single nucleotide polymorphism (SNP) data for 426 individuals from 25 sites, we further investigated sex-specific landscape and climatic effects on neutral genetic connectivity and migration patterns. We found evidence for sex differences associated with the I. elegans range expansion, namely (a) increased male body size with latitude, but no latitudinal effect on female body size, resulting in reduced sexual dimorphism towards the range limit, (b) a steeper decline in male genetic similarity with increasing geographic distance than in females, (c) male-biased genetic migration propensity and (d) a latitudinal cline in migration distance (increasing migratory distances towards the range margin), which was stronger in males. Cooler mean annual temperatures towards the range limit were associated with increased resistance to gene flow in both sexes. Sex ratios became increasingly male biased towards the range limit, and there was evidence for a changed sexual selection regime shifting from favouring larger males in the south to favouring smaller males in the north. Our findings suggest sex-specific spatial phenotype sorting at the range limit, where larger males disperse more under higher landscape resistance associated with cooler climates. The combination of latitudinal gradients in sex-biased dispersal, increasing male body size and (reduced) sexual size dimorphism should have emergent consequences for sexual selection dynamics and the mating system at the expanding range front. Our study illustrates the importance of considering sex differences in the study of range expansions driven by ongoing climate change.
Collapse
Affiliation(s)
- Rachael Y Dudaniec
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Alexander R Carey
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia.,Department of Planning, Industry and Environment, Saving our Species Program, New South Wales Government, Sydney, NSW, Australia
| | | | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
| | - Chuan Ji Yong
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Lesley T Lancaster
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK
| |
Collapse
|
11
|
Mettke-Hofmann C, Eccles GR, Greggor AL, Bethell EJ. Cognition in a Changing World: Red-Headed Gouldian Finches Enter Spatially Unfamiliar Habitats More Readily Than Do Black-Headed Birds. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.498347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
12
|
Klass K, Van Belle S, Campos-Villanueva A, Mercado Malabet F, Estrada A. Effects of variation in forest fragment habitat on black howler monkey demography in the unprotected landscape around Palenque National Park, Mexico. PeerJ 2020; 8:e9694. [PMID: 32864215 PMCID: PMC7425640 DOI: 10.7717/peerj.9694] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 07/20/2020] [Indexed: 11/20/2022] Open
Abstract
Habitat loss and fragmentation are leading threats to biodiversity today, and primates are particularly vulnerable to anthropogenic habitat disturbance. However, few studies have examined how differential effects of variation in forest fragment characteristics on males and females in a primate population may affect demography and population persistence. We quantified the effects of variation in forest fragment characteristics on the within-fragment demography of black howler monkeys (Alouatta pigra) in forest fragments around Palenque National Park, Mexico, and how these effects differed between adult males and females. We quantified forest loss in the landscape between 2000 and 2017, and used a redundancy analysis to examine the effects of 15 variables quantifying fragment dimensions, forest composition and physical structure, and isolation on fragment population size and density, the proportion of adult males and females in the fragment population, and the mean number of adult males and females per group in 34 fragments (N = 393 monkeys). We hypothesized that (i) population size is positively correlated with fragment area, while population density is negatively correlated, and (ii) the composition of fragment populations results from differential effects of fragment variables on adult males and females. Forest cover decreased by 23.3% from 2000 to 2017. Our results showed a significant effect of fragment variables on population demography in fragments, accounting for 0.69 of the variance in the demographic response variables. Population size increased with fragment area and connectivity, while density decreased. Larger, less isolated fragments with better connectivity, characteristics indicative of abundant secondary growth, and those with more diverse vegetation but lower Simpson’s evenness indices tended to have more adult females per group and a higher proportion of adult females in the population. In contrast, fragments that were largely similar in characteristics of forest composition and structure, but that were more isolated from nearby fragments, had more adult males per group and a higher proportion of adult males. These results may stem from black howler females preferentially remaining in natal groups and fragments when possible, and dispersing shorter distances when they disperse, while males may be more likely to disperse between fragments, traveling longer distances through the matrix to more isolated fragments. These differential effects on males and females have important conservation implications: if females are more abundant in larger, less isolated fragments, while males are more abundant in more isolated fragments, then to effectively conserve this population, both landscape connectivity and fragment areas should be maintained and increased.
Collapse
Affiliation(s)
- Keren Klass
- Department of Anthropology, University of Toronto, Toronto, ON, Canada.,Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Sarie Van Belle
- Department of Anthropology, University of Texas at Austin, Austin, TX, USA
| | | | | | - Alejandro Estrada
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
13
|
García J, Morán‐Ordóñez A, García JT, Calero‐Riestra M, Alda F, Sanz J, Suárez‐Seoane S. Current landscape attributes and landscape stability in breeding grounds explain genetic differentiation in a long‐distance migratory bird. Anim Conserv 2020. [DOI: 10.1111/acv.12616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J. García
- Department of Biodiversity and Environmental Management University of León León Spain
| | | | - J. T. García
- Instituto de Investigación en Recursos Cinegéticos (CSIC‐UCLM‐JCCM) Ciudad Real Spain
| | - M. Calero‐Riestra
- Instituto de Investigación en Recursos Cinegéticos (CSIC‐UCLM‐JCCM) Ciudad Real Spain
| | - F. Alda
- Department of Biology, Geology, and Environmental Science University of Tennessee at Chattanooga Chattanooga TN USA
| | - J. Sanz
- Laboratorio de Teledetección de la Universidad de Valladolid (LATUV) Valladolid Spain
| | - S. Suárez‐Seoane
- Department of Organisms and Systems Biology (BOS: Ecology Unit) Research Unit of Biodiversity (UMIBUO‐CSIC‐PA)University of Oviedo Oviedo Spain
| |
Collapse
|
14
|
Gan HM, Falk S, Morales HE, Austin CM, Sunnucks P, Pavlova A. Genomic evidence of neo-sex chromosomes in the eastern yellow robin. Gigascience 2019; 8:giz111. [PMID: 31494668 PMCID: PMC6736294 DOI: 10.1093/gigascience/giz111] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/31/2019] [Accepted: 08/14/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Understanding sex-biased natural selection can be enhanced by access to well-annotated chromosomes including ones inherited in sex-specific fashion. The eastern yellow robin (EYR) is an endemic Australian songbird inferred to have experienced climate-driven sex-biased selection and is a prominent model for studying mitochondrial-nuclear interactions in the wild. However, the lack of an EYR reference genome containing both sex chromosomes (in birds, a female bearing Z and W chromosomes) limits efforts to understand the mechanisms of these processes. Here, we assemble the genome for a female EYR and use low-depth (10×) genome resequencing data from 19 individuals of known sex to identify chromosome fragments with sex-specific inheritance. FINDINGS MaSuRCA hybrid assembly using Nanopore and Illumina reads generated a 1.22-Gb EYR genome in 20,702 scaffolds (94.2% BUSCO completeness). Scaffolds were tested for W-linked (female-only) inheritance using a k-mer approach, and for Z-linked inheritance using median read-depth test in male and female reads (read-depths must indicate haploid female and diploid male representation). This resulted in 2,372 W-linked scaffolds (total length: 97,872,282 bp, N50: 81,931 bp) and 586 Z-linked scaffolds (total length: 121,817,358 bp, N50: 551,641 bp). Anchoring of the sex-linked EYR scaffolds to the reference genome of a female zebra finch revealed 2 categories of sex-linked genomic regions. First, 653 W-linked scaffolds (25.7 Mb) were anchored to the W sex chromosome and 215 Z-linked scaffolds (74.4 Mb) to the Z. Second, 1,138 W-linked scaffolds (70.9 Mb) and 179 Z-linked scaffolds (51.0 Mb) were anchored to a large section (coordinates ∼5 to ∼60 Mb) of zebra finch chromosome 1A. The first ∼5 Mb and last ∼14 Mb of the reference chromosome 1A had only autosomally behaving EYR scaffolds mapping to them. CONCLUSIONS We report a female (W chromosome-containing) EYR genome and provide genomic evidence for a neo-sex (neo-W and neo-Z) chromosome system in the EYR, involving most of a large chromosome (1A) previously only reported to be autosomal in passerines.
Collapse
Affiliation(s)
- Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3220, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Victoria 3220, Australia
| | - Stephanie Falk
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, Victoria 3800, Australia
| | - Hernán E Morales
- Centre for Marine Evolutionary Biology, Department of Marine Sciences, University of Gothenburg, Göteborg 405 30, Sweden
| | - Christopher M Austin
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3220, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Victoria 3220, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, Victoria 3800, Australia
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, Victoria 3800, Australia
| |
Collapse
|
15
|
Blanton RE, Cashner MF, Thomas MR, Brandt SL, Floyd MA. Increased habitat fragmentation leads to isolation among and low genetic diversity within populations of the imperiled Kentucky Arrow Darter (Etheostoma sagitta spilotum). CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01188-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
16
|
László Z, Dénes AL, Király L, Tóthmérész B. Biased parasitoid sex ratios: Wolbachia, functional traits, local and landscape effects. Basic Appl Ecol 2018. [DOI: 10.1016/j.baae.2018.05.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
17
|
Stevens K, Harrisson KA, Hogan FE, Cooke R, Clarke RH. Reduced gene flow in a vulnerable species reflects two centuries of habitat loss and fragmentation. Ecosphere 2018. [DOI: 10.1002/ecs2.2114] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Kate Stevens
- Centre for Integrative Ecology; School of Life and Environmental Sciences; Deakin University; Geelong Victoria 3220 Australia
| | - Katherine A. Harrisson
- School of Biological Sciences; Monash University; Melbourne Victoria 3168 Australia
- Department of Ecology Environment and Evolution; School of Life Sciences; La Trobe University; Bundoora Victoria 3083 Australia
- Arthur Rylah Institute for Environmental Research; Heidelberg Victoria 3084 Australia
| | - Fiona E. Hogan
- School of Applied and Biomedical Sciences; Federation University Australia; Churchill Victoria 3842 Australia
| | - Raylene Cooke
- Centre for Integrative Ecology; School of Life and Environmental Sciences; Deakin University; Geelong Victoria 3220 Australia
| | - Rohan H. Clarke
- School of Biological Sciences; Monash University; Melbourne Victoria 3168 Australia
| |
Collapse
|
18
|
Mims MC, Hartfield Kirk EE, Lytle DA, Olden JD. Traits-based approaches support the conservation relevance of landscape genetics. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1028-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
19
|
Garcia VOS, Ivy C, Fu J. Syntopic frogs reveal different patterns of interaction with the landscape: A comparative landscape genetic study of Pelophylax nigromaculatus and Fejervarya limnocharis from central China. Ecol Evol 2017; 7:9294-9306. [PMID: 29187969 PMCID: PMC5696414 DOI: 10.1002/ece3.3459] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/04/2017] [Accepted: 08/11/2017] [Indexed: 01/05/2023] Open
Abstract
Amphibians are often considered excellent environmental indicator species. Natural and man‐made landscape features are known to form effective genetic barriers to amphibian populations; however, amphibians with different characteristics may have different species–landscape interaction patterns. We conducted a comparative landscape genetic analysis of two closely related syntopic frog species from central China, Pelophylax nigromaculatus (PN) and Fejervarya limnocharis (FL). These two species differ in several key life history traits; PN has a larger body size and larger clutch size, and reaches sexual maturity later than FL. Microsatellite DNA data were collected and analyzed using conventional (FST, isolation by distance (IBD), AMOVA) and recently developed (Bayesian assignment test, isolation by resistance) landscape genetic methods. As predicted, a higher level of population structure in FL (FST′ = 0.401) than in PN (FST′ = 0.354) was detected, in addition to FL displaying strong IBD patterns (r = .861) unlike PN (r = .073). A general north–south break in FL populations was detected, consistent with the IBD pattern, while PN exhibited clustering of northern‐ and southern‐most populations, suggestive of altered dispersal patterns. Species‐specific resistant landscape features were also identified, with roads and land cover the main cause of resistance to FL, and elevation the main influence on PN. These different species–landscape interactions can be explained mostly by their life history traits, revealing that closely related and ecologically similar species have different responses to the same landscape features. Comparative landscape genetic studies are important in detecting such differences and refining generalizations about amphibians in monitoring environmental changes.
Collapse
Affiliation(s)
| | - Catherine Ivy
- Department of Integrative Biology University of Guelph Guelph ON Canada.,Present address: Department of Biology McMaster University Hamilton ON Canada
| | - Jinzhong Fu
- Department of Integrative Biology University of Guelph Guelph ON Canada
| |
Collapse
|
20
|
Soanes K, Taylor AC, Sunnucks P, Vesk PA, Cesarini S, Ree R. Evaluating the success of wildlife crossing structures using genetic approaches and an experimental design: Lessons from a gliding mammal. J Appl Ecol 2017. [DOI: 10.1111/1365-2664.12966] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Kylie Soanes
- School of Ecosystem and Forest Sciences The University of Melbourne Parkville Vic. Australia
| | - Andrea C. Taylor
- School of Biological Sciences Monash University Clayton Vic. Australia
| | - Paul Sunnucks
- School of Biological Sciences Monash University Clayton Vic. Australia
| | - Peter A. Vesk
- School of BioSciences The University of Melbourne Parkville Vic. Australia
| | - Silvana Cesarini
- School of Biological Sciences Monash University Clayton Vic. Australia
| | - Rodney Ree
- School of BioSciences The University of Melbourne Parkville Vic. Australia
- Ecology and Infrastructure International Wantirna Vic. Australia
| |
Collapse
|
21
|
Tucker JM, Allendorf FW, Truex RL, Schwartz MK. Sex‐biased dispersal and spatial heterogeneity affect landscape resistance to gene flow in fisher. Ecosphere 2017. [DOI: 10.1002/ecs2.1839] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Jody M. Tucker
- Sequoia National Forest U.S. Forest Service, Pacific Southwest Region 1839 S. Newcomb Street Porterville California 93257 USA
| | - Fred W. Allendorf
- Division of Biological Sciences University of Montana 32 Campus Drive Missoula Montana 59812 USA
| | - Richard L. Truex
- U.S. Forest Service, Rocky Mountain Region 1617 Cole Boulevard Lakewood Colorado 80401 USA
| | - Michael K. Schwartz
- U.S. Forest Service, Rocky Mountain Research Station 800 East Beckwith Avenue Missoula Montana 59801 USA
| |
Collapse
|
22
|
Bertrand P, Bowman J, Dyer RJ, Manseau M, Wilson PJ. Sex-specific graphs: Relating group-specific topology to demographic and landscape data. Mol Ecol 2017; 26:3898-3912. [PMID: 28488269 DOI: 10.1111/mec.14174] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 04/24/2017] [Accepted: 04/25/2017] [Indexed: 02/01/2023]
Abstract
Sex-specific genetic structure is a commonly observed pattern among vertebrate species. Facing differential selective pressures, individuals may adopt sex-specific life history traits that ultimately shape genetic variation among populations. Although differential dispersal dynamics are commonly detected in the literature, few studies have used genetic structure to investigate sex-specific functional connectivity. The recent use of graph theoretic approaches in landscape genetics has demonstrated network capacities to describe complex system behaviours where network topology represents genetic interaction among subunits. Here, we partition the overall genetic structure into sex-specific graphs, revealing different male and female dispersal dynamics of a fisher (Pekania [Martes] pennanti) metapopulation in southern Ontario. Our analyses based on network topologies supported the hypothesis of male-biased dispersal. Furthermore, we demonstrated that the effect of the landscape, identified at the population level, could be partitioned among sex-specific strata. We found that female connectivity was negatively correlated with snow depth, whereas connectivity among males was not. Our findings underscore the potential of conducting sex-specific analysis by identifying landscape elements or configuration that differentially promotes or impedes functional connectivity between sexes, revealing processes that may otherwise remain cryptic. We propose that the sex-specific graph approach would be applicable to other vagile species where differential sex-specific processes are expected to occur.
Collapse
Affiliation(s)
- Philip Bertrand
- Département de Biologie, Chimie & Géographie, Université du Québec à Rimouski, Rimouski, QC, Canada
| | - Jeff Bowman
- Wildlife Research & Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Trent University, Peterborough, ON, Canada
| | - Rodney J Dyer
- Center for Environmental Studies, Virginia Commonwealth University, Richmond, VA, USA
| | - Micheline Manseau
- Office of the Chief Ecosystem Scientist, Gatineau, QC, Canada.,Natural Resources Institute, University of Manitoba, Winnipeg, MB, Canada
| | - Paul J Wilson
- Biology Department, Trent University, Peterborough, ON, Canada
| |
Collapse
|
23
|
Johnson CD, Evans D, Jones D. Birds and Roads: Reduced Transit for Smaller Species over Roads within an Urban Environment. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00036] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
24
|
Morales HE, Sunnucks P, Joseph L, Pavlova A. Perpendicular axes of differentiation generated by mitochondrial introgression. Mol Ecol 2017; 26:3241-3255. [DOI: 10.1111/mec.14114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 03/14/2017] [Accepted: 03/15/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Hernán E. Morales
- School of Biological Sciences Monash UniversityClayton Campus Melbourne Vic. 3800 Australia
- Centre for Marine Evolutionary Biology Department of Marine Sciences University of GothenburgBox 461 SE 405 30 Göteborg Sweden
| | - Paul Sunnucks
- School of Biological Sciences Monash UniversityClayton Campus Melbourne Vic. 3800 Australia
| | - Leo Joseph
- Australian National Wildlife Collection CSIRO National Research Collections AustraliaGPO Box 1700 Canberra ACT 2601 Australia
| | - Alexandra Pavlova
- School of Biological Sciences Monash UniversityClayton Campus Melbourne Vic. 3800 Australia
| |
Collapse
|
25
|
Johnson JS, Gaddis KD, Cairns DM, Konganti K, Krutovsky KV. Landscape genomic insights into the historic migration of mountain hemlock in response to Holocene climate change. AMERICAN JOURNAL OF BOTANY 2017; 104:439-450. [PMID: 28325831 DOI: 10.3732/ajb.1600262] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 02/17/2017] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Untangling alternative historic dispersal pathways in long-lived tree species is critical to better understand how temperate tree species may respond to climatic change. However, disentangling these alternative pathways is often difficult. Emerging genomic technologies and landscape genetics techniques improve our ability to assess these pathways in natural systems. We address the question to what degree have microrefugial patches and long-distance dispersal been responsible for the colonization of mountain hemlock (Tsuga mertensiana) on the Alaskan Kenai Peninsula. METHODS We used double-digest restriction-associated DNA sequencing (ddRADseq) to identify genetic variants across eight mountain hemlock sample sites on the Kenai Peninsula, Alaska. We assessed genetic diversity and linkage disequilibrium using landscape and population genetics approaches. Alternative historic dispersal pathways were assessed using discriminant analysis of principle components and electrical circuit theory. KEY RESULTS A combination of decreasing diversity, high gene flow, and landscape connectivity indicates that mountain hemlock colonization on the Kenai Peninsula is the result of long-distance dispersal. We found that contemporary climate best explained gene flow patterns and that isolation by resistance was a better model explaining genetic variation than isolation by distance. CONCLUSIONS Our findings support the conclusion that mountain hemlock colonization is the result of several long-distance dispersal events following Pleistocene glaciation. The high dispersal capability suggests that mountain hemlock may be able to respond to future climate change and expand its range as new habitat opens along its northern distribution.
Collapse
Affiliation(s)
- Jeremy S Johnson
- Department of Geography, Texas A&M University, 810 Eller O&M Building, MS 3147 TAMU, College Station, Texas 77843-3147 USA
| | - Keith D Gaddis
- Department of Geography, Texas A&M University, 810 Eller O&M Building, MS 3147 TAMU, College Station, Texas 77843-3147 USA
| | - David M Cairns
- Department of Geography, Texas A&M University, 810 Eller O&M Building, MS 3147 TAMU, College Station, Texas 77843-3147 USA
| | - Kranti Konganti
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University Veterinary Medical Research Building, MS 2470 TAMU, College Station, Texas 77433-2470 USA
| | - Konstantin V Krutovsky
- Department of Forest Genetics and Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, D-37077 Göttingen, Germany
- Department of Ecosystem Science & Management, Texas A&M University, 305 Horticulture and Forest Science Building, MS 2138 TAMU, College Station, Texas 77843-2138 USA
- N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina Str., Moscow 119333, Russia
- Genome Research and Education Center, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk 660036, Russia
| |
Collapse
|
26
|
|
27
|
Larroque J, Ruette S, Vandel JM, Queney G, Devillard S. Age and sex-dependent effects of landscape cover and trapping on the spatial genetic structure of the stone marten (Martes foina). CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0862-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
28
|
Balasubramaniam S, Bray RD, Mulder RA, Sunnucks P, Pavlova A, Melville J. New data from basal Australian songbird lineages show that complex structure of MHC class II β genes has early evolutionary origins within passerines. BMC Evol Biol 2016; 16:112. [PMID: 27206579 PMCID: PMC4875725 DOI: 10.1186/s12862-016-0681-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 05/10/2016] [Indexed: 11/10/2022] Open
Abstract
Background The major histocompatibility complex (MHC) plays a crucial role in the adaptive immune system and has been extensively studied across vertebrate taxa. Although the function of MHC genes appears to be conserved across taxa, there is great variation in the number and organisation of these genes. Among avian species, for instance, there are notable differences in MHC structure between passerine and non-passerine lineages: passerines typically have a high number of highly polymorphic MHC paralogs whereas non-passerines have fewer loci and lower levels of polymorphism. Although the occurrence of highly polymorphic MHC paralogs in passerines is well documented, their evolutionary origins are relatively unexplored. The majority of studies have focussed on the more derived passerine lineages and there is very little empirical information on the diversity of the MHC in basal passerine lineages. We undertook a study of MHC diversity and evolutionary relationships across seven species from four families (Climacteridae, Maluridae, Pardalotidae, Meliphagidae) that comprise a prominent component of the basal passerine lineages. We aimed to determine if highly polymorphic MHC paralogs have an early evolutionary origin within passerines or are a more derived feature of the infraorder Passerida. Results We identified 177 alleles of the MHC class II β exon 2 in seven basal passerine species, with variation in numbers of alleles across individuals and species. Overall, we found evidence of multiple gene loci, pseudoalleles, trans-species polymorphism and high allelic diversity in these basal lineages. Phylogenetic reconstruction of avian lineages based on MHC class II β exon 2 sequences strongly supported the monophyletic grouping of basal and derived passerine species. Conclusions Our study provides evidence of a large number of highly polymorphic MHC paralogs in seven basal passerine species, with strong similarities to the MHC described in more derived passerine lineages rather than the simpler MHC in non-passerine lineages. These findings indicate an early evolutionary origin of highly polymorphic MHC paralogs in passerines and shed light on the evolutionary forces shaping the avian MHC. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0681-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Shandiya Balasubramaniam
- Department of Sciences, Museum Victoria, Melbourne, VIC, 3001, Australia. .,School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Rebecca D Bray
- Terrestrial Vertebrates, Western Australian Museum, Perth, WA, 6986, Australia
| | - Raoul A Mulder
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Jane Melville
- Department of Sciences, Museum Victoria, Melbourne, VIC, 3001, Australia
| |
Collapse
|
29
|
Wultsch C, Waits LP, Kelly MJ. A Comparative Analysis of Genetic Diversity and Structure in Jaguars (Panthera onca), Pumas (Puma concolor), and Ocelots (Leopardus pardalis) in Fragmented Landscapes of a Critical Mesoamerican Linkage Zone. PLoS One 2016; 11:e0151043. [PMID: 26974968 PMCID: PMC4790928 DOI: 10.1371/journal.pone.0151043] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 02/23/2016] [Indexed: 01/23/2023] Open
Abstract
With increasing anthropogenic impact and landscape change, terrestrial carnivore populations are becoming more fragmented. Thus, it is crucial to genetically monitor wild carnivores and quantify changes in genetic diversity and gene flow in response to these threats. This study combined the use of scat detector dogs and molecular scatology to conduct the first genetic study on wild populations of multiple Neotropical felids coexisting across a fragmented landscape in Belize, Central America. We analyzed data from 14 polymorphic microsatellite loci in 1053 scat samples collected from wild jaguars (Panthera onca), pumas (Puma concolor), and ocelots (Leopardus pardalis). We assessed levels of genetic diversity, defined potential genetic clusters, and examined gene flow for the three target species on a countrywide scale using a combination of individual- and population-based analyses. Wild felids in Belize showed moderate levels of genetic variation, with jaguars having the lowest diversity estimates (HE = 0.57 ± 0.02; AR = 3.36 ± 0.09), followed by pumas (HE = 0.57 ± 0.08; AR = 4.20 ± 0.16), and ocelots (HE = 0.63 ± 0.03; AR = 4.16 ± 0.08). We observed low to moderate levels of genetic differentiation for all three target species, with jaguars showing the lowest degree of genetic subdivision across the country, followed by ocelots and pumas. Although levels of genetic diversity and gene flow were still fairly high, we detected evidence of fine-scale genetic subdivision, indicating that levels of genetic connectivity for wild felids in Belize are likely to decrease if habitat loss and fragmentation continue at the current rate. Our study demonstrates the value of understanding fine-scale patterns of gene flow in multiple co-occurring felid species of conservation concern, which is vital for wildlife movement corridor planning and prioritizing future conservation and management efforts within human-impacted landscapes.
Collapse
Affiliation(s)
- Claudia Wultsch
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Marcella J. Kelly
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, United States of America
| |
Collapse
|
30
|
Kvistad L, Ingwersen D, Pavlova A, Bull JK, Sunnucks P. Very Low Population Structure in a Highly Mobile and Wide-Ranging Endangered Bird Species. PLoS One 2015; 10:e0143746. [PMID: 26649426 PMCID: PMC4674126 DOI: 10.1371/journal.pone.0143746] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 11/09/2015] [Indexed: 11/18/2022] Open
Abstract
The loss of biodiversity following fragmentation and degradation of habitat is a major issue in conservation biology. As competition for resources increases following habitat loss and fragmentation, severe population declines may occur even in common, highly mobile species; such demographic decline may cause changes within the population structure of the species. The regent honeyeater, Anthochaera phrygia, is a highly nomadic woodland bird once common in its native southeast Australia. It has experienced a sharp decline in abundance since the late 1970s, following clearing of large areas of its preferred habitat, box-ironbark woodland, within the last 200 years. A captive breeding program has been established as part of efforts to restore this species. This study used genetic data to examine the range-wide population structure of regent honeyeaters, including spatial structure, its change through time, sex differences in philopatry and mobility, and genetic differences between the captive and wild populations. There was low genetic differentiation between birds captured in different geographic areas. Despite the recent demographic decline, low spatial structure appears to have some temporal consistency. Both sexes appear to be highly mobile, and there does not seem to be significant genetic differentiation between the captive and wild populations. We conclude that management efforts for survival of this species, including habitat protection, restoration, and release of captive-bred birds into the wild, can treat the species as effectively a single genetic population.
Collapse
Affiliation(s)
- Lynna Kvistad
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | | | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - James K. Bull
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| |
Collapse
|
31
|
Epps CW, Keyghobadi N. Landscape genetics in a changing world: disentangling historical and contemporary influences and inferring change. Mol Ecol 2015; 24:6021-40. [DOI: 10.1111/mec.13454] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 10/29/2015] [Accepted: 11/02/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Clinton W. Epps
- Oregon State University; Nash Hall Room 104 Corvallis OR 97331 USA
| | - Nusha Keyghobadi
- Department of Biology; Western University; London ON N6A 5B7 Canada
| |
Collapse
|
32
|
Gene Flow of a Forest-Dependent Bird across a Fragmented Landscape. PLoS One 2015; 10:e0140938. [PMID: 26580222 PMCID: PMC4651334 DOI: 10.1371/journal.pone.0140938] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 09/30/2015] [Indexed: 02/01/2023] Open
Abstract
Habitat loss and fragmentation can affect the persistence of populations by reducing connectivity and restricting the ability of individuals to disperse across landscapes. Dispersal corridors promote population connectivity and therefore play important roles in maintaining gene flow in natural populations inhabiting fragmented landscapes. In the prairies, forests are restricted to riparian areas along river systems which act as important dispersal corridors for forest dependent species across large expanses of unsuitable grassland habitat. However, natural and anthropogenic barriers within riparian systems have fragmented these forested habitats. In this study, we used microsatellite markers to assess the fine-scale genetic structure of a forest-dependent species, the black-capped chickadee (Poecile atricapillus), along 10 different river systems in Southern Alberta. Using a landscape genetic approach, landscape features (e.g., land cover) were found to have a significant effect on patterns of genetic differentiation. Populations are genetically structured as a result of natural breaks in continuous habitat at small spatial scales, but the artificial barriers we tested do not appear to restrict gene flow. Dispersal between rivers is impeded by grasslands, evident from isolation of nearby populations (~ 50 km apart), but also within river systems by large treeless canyons (>100 km). Significant population genetic differentiation within some rivers corresponded with zones of different cottonwood (riparian poplar) tree species and their hybrids. This study illustrates the importance of considering the impacts of habitat fragmentation at small spatial scales as well as other ecological processes to gain a better understanding of how organisms respond to their environmental connectivity. Here, even in a common and widespread songbird with high dispersal potential, small breaks in continuous habitats strongly influenced the spatial patterns of genetic variation.
Collapse
|
33
|
Ferrer ES, García-Navas V, Bueno-Enciso J, Barrientos R, Serrano-Davies E, Cáliz-Campal C, Sanz JJ, Ortego J. The influence of landscape configuration and environment on population genetic structure in a sedentary passerine: insights from loci located in different genomic regions. J Evol Biol 2015; 29:205-19. [DOI: 10.1111/jeb.12776] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 10/07/2015] [Accepted: 10/12/2015] [Indexed: 11/29/2022]
Affiliation(s)
- E. S. Ferrer
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM); Ciudad Real Spain
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - V. García-Navas
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM); Ciudad Real Spain
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
- Institute of Evolutionary Biology and Environmental Studies; University of Zurich; Zurich Switzerland
| | - J. Bueno-Enciso
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - R. Barrientos
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - E. Serrano-Davies
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - C. Cáliz-Campal
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM); Ciudad Real Spain
- Department of Integrative Ecology; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
| | - J. J. Sanz
- Departamento de Ecología Evolutiva; Museo Nacional de Ciencias Naturales (CSIC); Madrid Spain
| | - J. Ortego
- Department of Integrative Ecology; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
| |
Collapse
|
34
|
Murphy AL, Pavlova A, Thompson R, Davis J, Sunnucks P. Swimming through sand: connectivity of aquatic fauna in deserts. Ecol Evol 2015; 5:5252-5264. [PMID: 30151128 PMCID: PMC6102528 DOI: 10.1002/ece3.1741] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 08/11/2015] [Accepted: 08/22/2015] [Indexed: 01/15/2023] Open
Abstract
Freshwater ecosystems in arid regions range from highly fragmented to highly connected, and connectivity has been assumed to be a major factor in the persistence of aquatic biota in arid environments. This review sought to synthesize existing research on genetic estimation of population connectivity in desert freshwaters, identify knowledge gaps, and set priorities for future studies of connectivity in these environments. From an extensive literature search, we synthesized the approaches applied, systems studied, and conclusions about connectivity reached in population genetic research concerning desert freshwater connectivity globally. We restrict our scope to obligate aquatic fauna that disperse largely via freshwaters and exclude those with active aerial dispersal abilities. We examined 92 papers, comprising 133 studies, published from 1987 to 2014. Most described studies of fishes and invertebrates in the deserts of Australia and North America. Connectivity declined with increasing scale, but did not differ significantly among arid regions or taxonomic classes. There were significant differences in connectivity patterns between species with different dispersal abilities, and between spring and riverine habitats at local scales. Population connectivity in desert freshwaters is typically most influenced by the ecology of the species concerned and hydrological connectivity. Most studies did not assess predefined models of connectivity, but described gene flow and/or genetic structure. Climate change and anthropogenic impacts worldwide are likely to increase the incidence and impact of habitat fragmentation in already threatened desert freshwaters. To reduce this risk, biodiversity conservation and environmental management must address connectivity, but often the required information does not exist. Researchers can provide this by explicitly considering the effects of hydrology and species' ecology on connectivity, and incorporating these into connectivity models, which are vital for understanding connectivity in desert freshwaters.
Collapse
Affiliation(s)
- Ashley L Murphy
- School of Biological Sciences Monash University Melbourne Victoria 3800 Australia
| | - Alexandra Pavlova
- School of Biological Sciences Monash University Melbourne Victoria 3800 Australia
| | - Ross Thompson
- Institute for Applied Ecology University of Canberra Canberra Australian Capital Territory 2617 Australia
| | - Jenny Davis
- Institute for Applied Ecology University of Canberra Canberra Australian Capital Territory 2617 Australia
| | - Paul Sunnucks
- School of Biological Sciences Monash University Melbourne Victoria 3800 Australia
| |
Collapse
|
35
|
Malekian M, Cooper SJB, Saint KM, Lancaster ML, Taylor AC, Carthew SM. Effects of landscape matrix on population connectivity of an arboreal mammal, Petaurus breviceps. Ecol Evol 2015; 5:3939-53. [PMID: 26442617 PMCID: PMC4588655 DOI: 10.1002/ece3.1675] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 07/30/2015] [Accepted: 07/30/2015] [Indexed: 11/09/2022] Open
Abstract
Ongoing habitat loss and fragmentation is considered a threat to biodiversity as it can create small, isolated populations that are at increased risk of extinction. Tree‐dependent species are predicted to be highly sensitive to forest and woodland loss and fragmentation, but few studies have tested the influence of different types of landscape matrix on gene flow and population structure of arboreal species. Here, we examine the effects of landscape matrix on population structure of the sugar glider (Petaurus breviceps) in a fragmented landscape in southeastern South Australia. We collected 250 individuals across 12 native Eucalyptus forest remnants surrounded by cleared agricultural land or exotic Pinus radiata plantations and a large continuous eucalypt forest. Fifteen microsatellite loci were genotyped and analyzed to infer levels of population differentiation and dispersal. Genetic differentiation among most forest patches was evident. We found evidence for female philopatry and restricted dispersal distances for females relative to males, suggesting there is male‐biased dispersal. Among the environmental variables, spatial variables including geographic location, minimum distance to neighboring patch, and degree of isolation were the most important in explaining genetic variation. The permeability of a cleared agricultural matrix to dispersing gliders was significantly higher than that of a pine matrix, with the gliders dispersing shorter distances across the latter. Our results added to previous findings for other species of restricted dispersal and connectivity due to habitat fragmentation in the same region, providing valuable information for the development of strategies to improve the connectivity of populations in the future.
Collapse
Affiliation(s)
- Mansoureh Malekian
- Department of Natural Resources Isfahan University of Technology Isfahan 84156-83111 Iran ; School of Biological Sciences The University of Adelaide Adelaide SA 5005 Australia ; Australian Centre for Evolutionary Biology and Biodiversity The University of Adelaide Adelaide SA 5005 Australia
| | - Steven J B Cooper
- School of Biological Sciences The University of Adelaide Adelaide SA 5005 Australia ; Australian Centre for Evolutionary Biology and Biodiversity The University of Adelaide Adelaide SA 5005 Australia ; Evolutionary Biology Unit South Australian Museum Adelaide SA 5000 Australia
| | - Kathleen M Saint
- Evolutionary Biology Unit South Australian Museum Adelaide SA 5000 Australia
| | | | - Andrea C Taylor
- School of Biological Sciences Monash University Clayton Victoria 3800 Australia
| | - Susan M Carthew
- School of Biological Sciences The University of Adelaide Adelaide SA 5005 Australia ; Research Institute for Environment and Livelihoods Charles Darwin University Darwin NT 0909 Australia
| |
Collapse
|
36
|
Morán-Ordóñez A, Pavlova A, Pinder AM, Sim L, Sunnucks P, Thompson RM, Davis J. Aquatic communities in arid landscapes: local conditions, dispersal traits and landscape configuration determine local biodiversity. DIVERS DISTRIB 2015. [DOI: 10.1111/ddi.12342] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Alejandra Morán-Ordóñez
- School of Biological Sciences; Monash University; Clayton 3800 Vic. Australia
- NERP Environmental Decisions Hub; School of BioSciences (building 2); The University of Melbourne; Parkville 3010 Vic. Australia
| | - Alexandra Pavlova
- School of Biological Sciences; Monash University; Clayton 3800 Vic. Australia
| | - Adrian M. Pinder
- Science and Conservation Division; Department of Parks and Wildlife; Kensington 6151 WA Australia
| | - Lien Sim
- School of Biological Sciences; Monash University; Clayton 3800 Vic. Australia
- Science and Conservation Division; Department of Parks and Wildlife; Kensington 6151 WA Australia
| | - Paul Sunnucks
- School of Biological Sciences; Monash University; Clayton 3800 Vic. Australia
| | - Ross M. Thompson
- School of Biological Sciences; Monash University; Clayton 3800 Vic. Australia
- Institute for Applied Ecology; University of Canberra; Canberra 2617 ACT Australia
| | - Jenny Davis
- Institute for Applied Ecology; University of Canberra; Canberra 2617 ACT Australia
| |
Collapse
|
37
|
Barr KR, Kus BE, Preston KL, Howell S, Perkins E, Vandergast AG. Habitat fragmentation in coastal southern California disrupts genetic connectivity in the cactus wren (Campylorhynchus brunneicapillus). Mol Ecol 2015; 24:2349-63. [DOI: 10.1111/mec.13176] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 03/20/2015] [Accepted: 03/25/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Kelly R. Barr
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 29101 USA
| | - Barbara E. Kus
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 29101 USA
| | - Kristine L. Preston
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 29101 USA
| | - Scarlett Howell
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 29101 USA
| | - Emily Perkins
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 29101 USA
| | - Amy G. Vandergast
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station, 4165 Spruance Road, Suite 200 San Diego CA 29101 USA
| |
Collapse
|
38
|
Husemann M, Cousseau L, Callens T, Matthysen E, Vangestel C, Hallmann C, Lens L. Post-fragmentation population structure in a cooperative breeding Afrotropical cloud forest bird: emergence of a source-sink population network. Mol Ecol 2015; 24:1172-87. [PMID: 25677704 DOI: 10.1111/mec.13105] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 01/29/2015] [Accepted: 02/04/2015] [Indexed: 11/27/2022]
Abstract
The impact of demographic parameters on the genetic population structure and viability of organisms is a long-standing issue in the study of fragmented populations. Demographic and genetic tools are now readily available to estimate census and effective population sizes and migration and gene flow rates with increasing precision. Here we analysed the demography and genetic population structure over a recent 15-year time span in five remnant populations of Cabanis's greenbul (Phyllastrephus cabanisi), a cooperative breeding bird in a severely fragmented cloud forest habitat. Contrary to our expectation, genetic admixture and effective population sizes slightly increased, rather than decreased between our two sampling periods. In spite of small effective population sizes in tiny forest remnants, none of the populations showed evidence of a recent population bottleneck. Approximate Bayesian modelling, however, suggested that differentiation of the populations coincided at least partially with an episode of habitat fragmentation. The ratio of meta-Ne to meta-Nc was relatively low for birds, which is expected for cooperative breeding species, while Ne /Nc ratios strongly varied among local populations. While the overall trend of increasing population sizes and genetic admixture may suggest that Cabanis's greenbuls increasingly cope with fragmentation, the time period over which these trends were documented is rather short relative to the average longevity of tropical species. Furthermore, the critically low Nc in the small forest remnants keep the species prone to demographic and environmental stochasticity, and it remains open if, and to what extent, its cooperative breeding behaviour helps to buffer such effects.
Collapse
Affiliation(s)
- M Husemann
- General Zoology, Institute of Biology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | | | | | | | | | | | | |
Collapse
|
39
|
Hand BK, Lowe WH, Kovach RP, Muhlfeld CC, Luikart G. Landscape community genomics: understanding eco-evolutionary processes in complex environments. Trends Ecol Evol 2015; 30:161-8. [DOI: 10.1016/j.tree.2015.01.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 01/06/2015] [Accepted: 01/07/2015] [Indexed: 10/24/2022]
|