Displaying publications 1 - 20 of 63 in total

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  1. Zheng Y, Yuan C, Matsushita N, Lian C, Geng Q
    Ecol Evol, 2023 Sep;13(9):e10565.
    PMID: 37753310 DOI: 10.1002/ece3.10565
    Cenococcum geophilum (C. geophilum) is a widely distributed ectomycorrhizal fungus that plays a crucial role in forest ecosystems worldwide. However, the specific ecological factors influencing its global distribution and how climate change will affect its range are still relatively unknown. In this study, we used the MaxEnt model optimized with the kuenm package to simulate changes in the distribution pattern of C. geophilum from the Last Glacial Maximum to the future based on 164 global distribution records and 17 environmental variables and investigated the key environmental factors influencing its distribution. We employed the optimal parameter combination of RM = 4 and FC = QPH, resulting in a highly accurate predictive model. Our study clearly shows that the mean temperature of the coldest quarter and annual precipitation are the key environmental factors influencing the suitable habitats of C. geophilum. Currently, appropriate habitats of C. geophilum are mainly distributed in eastern Asia, west-central Europe, the western seaboard and eastern regions of North America, and southeastern Australia, covering a total area of approximately 36,578,300 km2 globally. During the Last Glacial Maximum and the mid-Holocene, C. geophilum had a much smaller distribution area, being mainly concentrated in the Qinling-Huaihe Line region of China and eastern Peninsular Malaysia. As global warming continues, the future suitable habitat for C. geophilum is projected to shift northward, leading to an expected expansion of the suitable area from 9.21% to 21.02%. This study provides a theoretical foundation for global conservation efforts and biogeographic understanding of C. geophilum, offering new insights into its distribution patterns and evolutionary trends.
  2. Sitam FT, Salgado-Lynn M, Denel A, Panjang E, McEwing R, Lightson A, et al.
    Ecol Evol, 2023 Aug;13(8):e10373.
    PMID: 37593756 DOI: 10.1002/ece3.10373
    The Sunda pangolin (Manis javanica) is the most widely distributed Asian pangolin species, occurring across much of Southeast Asia and in southern China. It is classified as Critically Endangered and is one of the most trafficked mammals in the world, which not only negatively impacts wild Sunda pangolin populations but also poses a potential disease risk to other species, including humans and livestock. Here, we aimed to investigate the species' phylogeography across its distribution to improve our understanding of the species' evolutionary history, elucidate any taxonomic uncertainties and enhance the species' conservation genetic management and potential wildlife forensics applications. We sequenced mtDNA genomes from 23 wild Sunda pangolins of known provenance originating from Malaysia to fill sampling gaps in previous studies, particularly in Borneo. To conduct phylogenetic and population genetic analyses of Sunda pangolins across their range, we integrated these newly generated mitochondrial genomes with previously generated mtDNA and nuclear DNA data sets (RAD-seq SNP data). We identified an evolutionarily distinct mtDNA lineage in north Borneo, estimated to be ~1.6 million years divergent from lineages in west/south Borneo and the mainland, comparable to the divergence time from the Palawan pangolin. There appeared to be mitonuclear discordance, with no apparent genetic structure across Borneo based on analysis of nuclear SNPs. These findings are consistent with the 'out of Borneo hypothesis', whereby Sunda pangolins diversified in Borneo before subsequently migrating throughout Sundaland, and/or a secondary contact scenario between mainland and Borneo. We have elucidated possible taxonomic issues in the Sunda/Palawan pangolin complex and highlight the critical need for additional georeferenced samples to accurately apportion its range-wide genetic variation into appropriate taxonomic and conservation units. Additionally, these data have improved forensic identification testing involving these species and permit the implementation of geographic provenance testing in some scenarios.
  3. Ong SQ, Mat Jalaluddin NS, Yong KT, Ong SP, Lim KF, Azhar S
    Ecol Evol, 2023 Jun;13(6):e10212.
    PMID: 37325726 DOI: 10.1002/ece3.10212
    Natural history museum collections are the most important sources of information on the present and past biodiversity of our planet. Most of the information is primarily stored in analogue form, and digitization of the collections can provide further open access to the images and specimen data to address the many global challenges. However, many museums do not digitize their collections because of constraints on budgets, human resources, and technologies. To encourage the digitization process, we present a guideline that offers low-cost and technical knowledge solutions yet balances the quality of the work and outcomes. The guideline describes three phases of digitization, namely preproduction, production, and postproduction. The preproduction phase includes human resource planning and selecting the highest priority collections for digitization. In the preproduction phase, a worksheet is provided for the digitizer to document the metadata, as well as a list of equipment needed to set up a digitizer station to image the specimens and associated labels. In the production phase, we place special emphasis on the light and color calibrations, as well as the guidelines for ISO/shutter speed/aperture to ensure a satisfactory quality of the digitized output. Once the specimen and labels have been imaged in the production phase, we demonstrate an end-to-end pipeline that uses optical character recognition (OCR) to transfer the physical text on the labels into a digital form and document it in a worksheet cell. A nationwide capacity workshop is then conducted to impart the guideline, and pre- and postcourse surveys were conducted to assess the confidence and skills acquired by the participants. This paper also discusses the challenges and future work that need to be taken forward for proper digital biodiversity data management.
  4. Kunde MN, Barlow A, Klittich AM, Yakupova A, Patel RP, Fickel J, et al.
    Ecol Evol, 2023 Apr;13(4):e9969.
    PMID: 37082317 DOI: 10.1002/ece3.9969
    The sun bear Helarctos malayanus is one of the most endangered ursids, and to date classification of sun bear populations has been based almost exclusively on geographic distribution and morphology. The very few molecular studies focussing on this species were limited in geographic scope. Using archival and non-invasively collected sample material, we have added a substantial number of complete or near-complete mitochondrial genome sequences from sun bears of several range countries of the species' distribution. We here report 32 new mitogenome sequences representing sun bears from Cambodia, Thailand, Peninsular Malaysia, Sumatra, and Borneo. Reconstruction of phylogenetic relationships revealed two matrilines that diverged ~295 thousand years ago: one restricted to portions of mainland Indochina (China, Cambodia, Thailand; "Mainland clade"), and one comprising bears from Borneo, Sumatra, Peninsular Malaysia but also Thailand ("Sunda clade"). Generally recent coalescence times in the mitochondrial phylogeny suggest that recent or historical demographic processes have resulted in a loss of mtDNA variation. Additionally, analysis of our data in conjunction with shorter mtDNA sequences revealed that the Bornean sun bear, classified as a distinct subspecies (H. m. euryspilus), does not harbor a distinctive matriline. Further molecular studies of H. malayanus are needed, which should ideally include data from nuclear loci.
  5. Malik N, Edwards D, Freckleton RP
    Ecol Evol, 2023 Apr;13(4):e10004.
    PMID: 37091565 DOI: 10.1002/ece3.10004
    The Janzen-Connell hypothesis proposes that density and distance-dependent mortality generated by specialist natural enemies prevent competitive dominance. Much literature on Janzen-Connell mechanisms comes from the neotropics, and evidence of the role of distance and density-dependence is still relatively sparse. We tested the predictions of the Janzen-Connell hypothesis in a South-East Asian system dominated by mast fruiting species. We hypothesized that seedling survival would decrease with distance and density, seedling growth would increase, and herbivory would decrease, according to the predictions of the Janzen-Connell hypothesis. Experiments were conducted to determine the strength of the Janzen-Connell mechanism by manipulating the density and identity of tree species as a function of the distance from parent trees. Survival of conspecific seedlings was reduced near adult trees of one species, but not another. High densities of seedlings decreased the growth of conspecific seedlings of both species. In both species, herbivory rates decreased with distance in low-density areas. This study indicates that dipterocarp species experienced weak Janzen-Connell effects of distance and density dependence at the growth stage studied. Future studies in this system might focus on earlier life-history stages such as seeds and small seedlings, as well as studying mortality during mast-seeding events.
  6. Yao TL, Nazre M, McKey D, Jalonen R, Duminil J
    Ecol Evol, 2023 Mar;13(3):e9792.
    PMID: 36937066 DOI: 10.1002/ece3.9792
    Mangosteen (Garcinia mangostana var. mangostana) is a popular tropical fruit, yet many aspects of its biology and evolutionary history are little known. Its origin remains contentious, although recent findings suggest G. mangostana L. var. malaccensis (Hook. f.) Nazre (synonym: G. malaccensis Hook. f.) as the sole progenitor. We review hypotheses on the origin of mangosteen and clarify points that have been affected by errors of fact and interpretation. The narrow focus and lack of detail in published results make their interpretation difficult. When possible, we support our interpretations with field observations and examination of herbarium specimens. We outline the main biological traits (e.g., dioecy, facultative apomixis, and polyploidy) of mangosteen and its wild relatives to infer traits that might have evolved during domestication of mangosteen. We find no clear indication that apomixis and polyploidy evolved during domestication. Polyploidy is known in the wild relatives, but apomixis has not yet been demonstrated. Also, we propose a testable new evolutionary-ecological framework that we call "Forest-Dusun Interface" to infer processes in the origin of mangosteen. Dusun (Malay) refers to subsistence orchards in this context. Lastly, we propose future studies to address identified knowledge gaps.
  7. Duong TY, Nguyen NT, Tran DD, Le TH, Nor SAM
    Ecol Evol, 2023 Feb;13(2):e9845.
    PMID: 36820247 DOI: 10.1002/ece3.9845
    Population genetic structure of migratory fishes can reflect ecological and evolutionary processes. Pangasius krempfi is a critically important anadromous catfish in the Mekong River, and its migration pathways and genetic structure have attracted much interest. To investigate, we quantified the genetic diversity of this species using the control region (D-loop) and Cytochrome b (Cytb) of the mitochondrial genome. Fish were sampled (n = 91) along the Mekong tributaries from upstream to estuaries and coastal areas in the Mekong Delta and compared to three samples from Pakse (Laos). The D-loop haplotype (0.941 ± 0.014) and nucleotide diversity (0.0083 ± 0.0005) were high in all populations, but that of Cytb was low (0.331 ± 0.059 and 0.00063 ± 0.00011, respectively). No genetic difference was detected between populations, indicating strong gene flow and confirming a long migration distance for this species. Pangasius krempfi was not genetically structured according to geographical populations but was delineated into three haplogroups, suggesting multiple genetic lineages. The presence of haplogroups in each sampling location implies that migration downstream is random but parallel when the fish enter two river tributaries bifurcating from the main Mekong River. Individuals can also migrate along the coast, far from the estuaries, suggesting a longer migration path than previously reported, which is crucial for maintaining diverse genetic origin and migration pathways for P. krempfi.
  8. Sharma S, Chee-Yoong W, Kannan A, Rama Rao S, Abdul-Patah P, Ratnayeke S
    Ecol Evol, 2022 Dec;12(12):e9585.
    PMID: 36518624 DOI: 10.1002/ece3.9585
    Four species of otters occur in tropical Asia, and all face multiple threats to their survival. Studies of distribution and population trends of these otter species in Asia, where they occur sympatrically, are complicated by their elusive nature and difficulties with reliable identification of species in field surveys. In Malaysia, only three species, the smooth-coated otter, Asian small-clawed otter, and hairy-nosed otter have been reliably reported as residents. We designed a replicable and cost-efficient PCR-RFLP protocol to identify these three species. Using published reference sequences of mitochondrial regions, we designed and tested three PCR-RFLP protocols on DNA extracted from reference samples and 33 spraints of wild otters collected along the North Central Selangor Coast of Malaysia. We amplified and sequenced two fragments (450 and 200 bp) of the mt D-loop region and a 300-bp fragment of the mt ND4 gene using primer sets TanaD, TanaD-Mod, and OTR-ND4, respectively. Amplification products were digested with restriction enzymes to generate species-specific RFLP profiles. We analyzed the costs of all three protocols and compared these with the costs of sequencing for species identification. Amplification success was highest for the smallest PCR product, with the TanaD-Mod primer amplifying DNA from all 33 spraints. TanaD and OTR-ND4 primers amplified DNA from 60.6% and 63.6% spraints, respectively. PCR products of TanaD-Mod provided the expected species-specific RFLP profile for 32 (97%) of the spraints. PCR products of OTR-ND4 provided the expected RFLP profile for all 21 samples that amplified, but TanaD produced spurious bands and inconsistent RFLP profiles. The OTR-ND4 primer-enzyme protocol was the least expensive (437 USD) for processing 100 samples, followed by TanaD-Mod (455 USD). We suggest the use of both OTR-ND4 and TanaD-Mod protocols that show potential for highly efficient and reliable species identification from noninvasive genetic sampling of three Asian otter species. We expect our novel noninvasive PCR-RFLP analysis methods to facilitate population monitoring, ecological and behavioral studies on otters in tropical and subtropical Asia.
  9. Sheridan JA, Mendenhall CD, Yambun P
    Ecol Evol, 2022 Dec;12(12):e9589.
    PMID: 36523519 DOI: 10.1002/ece3.9589
    Climate change threatens biodiversity in a range of ways, including changing animal body sizes. Despite numerous examples of size declines related to increasing temperatures, patterns of size change are not universal, suggesting that one or more primary mechanisms impacting size change are unknown. Precipitation is likely to influence the size different from and in conjunction with changes in temperature, yet tests of the interaction between these variables are rare. In this study, we show that a crossover interaction between temperature and precipitation impacts the body size of frogs as the climate warms. Using more than 3000 museum frog specimens from Borneo and climate records spanning more than 100 years, we found that frogs are larger in wet conditions than in dry conditions at cool temperatures, suggesting that resource availability determines body size at colder temperature. Conversely, frogs are larger in dry conditions than in wet conditions at warm temperatures, resulting in a crossover to desiccation resistance as the main determinant of body size as climates warm. Our results demonstrate that global warming can alter the impact of precipitation on life-history traits. We suggest that increased attention be paid to such interactive effects of climate variables, to identify complex mechanisms driving climate-induced size changes.
  10. Liu KL, Tseng SP, Tatsuta H, Tsuji K, Tay JW, Singham GV, et al.
    Ecol Evol, 2022 Dec;12(12):e9660.
    PMID: 36582779 DOI: 10.1002/ece3.9660
    Global commerce and transportation facilitate the spread of invasive species. The African big-headed ant, Pheidole megacephala (Fabricius), has achieved worldwide distribution through globalization. Since the late 19th century, Taiwan has served as a major seaport because of its strategic location. The population genetic structure of P. megacephala in Taiwan is likely to be shaped by international trade and migration between neighboring islands. In this study, we investigated the population genetics of P. megacephala colonies sampled from four geographical regions in Taiwan and elucidated the population genetic structures of P. megacephala sampled from Taiwan, Okinawa, and Hawaii. We observed a low genetic diversity of P. megacephala across regions in Taiwan. Moreover, we noted low regional genetic differentiation and did not observe isolation by distance, implying that long-distance jump dispersal might have played a crucial role in the spread of P. megacephala. We sequenced the partial cytochrome oxidase I gene and observed three mitochondrial haplotypes (TW1-TW3). TW1 and TW3 most likely originated from populations within the species' known invasive range, suggesting that secondary introduction is the predominant mode of introduction for this invasive ant. TW2 represents a novel haplotype that was previously unreported in other regions. P. megacephala populations from Taiwan, Okinawa, and Hawaii exhibited remarkable genetic similarity, which may reflect their relative geographic proximity and the historical connectedness of the Asia-Pacific region.
  11. Trethowan LA, Arvidsson C, Bramley GLC
    Ecol Evol, 2022 Nov;12(11):e9467.
    PMID: 36340815 DOI: 10.1002/ece3.9467
    Dual effects of spatial distance and environment shape archipelagic floras. In Malesia, there are multiple environmental stressors associated with increasing uplands, drought, and metal-rich ultramafic soils. Here, we examine the contrasting impacts of multifactorial environmental stress and spatial distance upon Lamiaceae species distributions. We used a phylogenetic generalized mixed effects model of species occurrence across Malesia's taxonomic database working group areas from Peninsular Malaysia to New Guinea. Predictor variables were environmental stress, spatial distance between areas and two trait principal component axes responsible for increasing fruit and leaf size and a negative correlation between flower size and plant height. We found that Lamiaceae species with smaller fruits and leaves are more likely to tolerate environmental stress and become widely distributed across megadiverse Malesian islands. How global species distribution and diversification are shaped by multifactorial environmental stress requires further examination.
  12. Okuno S, Yin T, Nanami S, Matsuyama S, Kamiya K, Tan S, et al.
    Ecol Evol, 2022 Nov;12(11):e9536.
    PMID: 36440315 DOI: 10.1002/ece3.9536
    Community phylogenetic analysis is an effective approach to understanding the process of community formation. The phylogenetic tree of the species pool is reconstructed in the first step, and the phylogenetic tree obtained in the second step is used to analyze phylogenetic diversity. Sythetic trees have often been used in the construction of phylogenentic trees; however, in tropical rainforests with many closely related species, synthetic trees contain many unresolved nodes, which may affect the results of phylogenetic structure analysis. Here, we constructed a phylogenetic tree using DNA barcode sequences (rbcL, matK, trnH-psbA) for 737 tree species from the rainforests of Borneo, which have a high-species diversity and many closely related species. The phylogenetic tree had fewer polytomies and more branch length variations than the Phylocom synthetic trees. Comparison of community phylogenetic analyses indicated that values of the standardized effect size of mean pairwise distance (SES-MPD) were highly correlated between Phylocom and DNA barcode trees, but less so for the standardized effect size of mean nearest taxon distance (SES-MNTD), suggesting that caution is needed when using synthetic trees for communities containing many congeneric species, especially when using SES-MNTD. Simulation analysis suggested that spatial dependence on phylogenetic diversity is related to the phylogenetic signal of the species' habitat niche and the spatial structure of habitat, indicating the importance of detailed phylogeny in understanding community assembly processes.
  13. Yap FC, Høeg JT, Chan BKK
    Ecol Evol, 2022 Jul;12(7):e9057.
    PMID: 35813926 DOI: 10.1002/ece3.9057
    Symbiosis is increasingly recognized as being an important component in marine systems, and many such relationships are initiated when free-swimming larvae of one partner settle and become sedentary on a host partner. Therefore, several crucial questions emerge such as the larva's mechanism of locating a host, selection of substratum and finally settlement on the surface of its future partner. Here, we investigated these mechanisms by studying how larvae of the fire coral-associated barnacle Wanella milleporae move, settle and establish symbiosis with their host, Millepora tenera. Cyprids of W. milleporae possess a pair of specialized antennules with bell-shaped attachment discs that enable them to explore and settle superficially on the hostile surface of the fire coral. Intriguingly, the stinging polyps of the fire coral remain in their respective pores when the cyprids explore the fire coral surface. Even when cyprids come into contact with the nematocysts on the extended stinging polyps during the exploratory phase, no immobilization effects against the cyprids were observed. The exploratory phase of Wanella cyprids can be divided into a sequence of wide searching (large step length and high walking speed), close searching (small step length and low speed) and inspection behavior, eventually resulting in permanent settlement and metamorphosis. After settlement, xenogeneic interactions occur between the fire coral and the newly metamorphosed juvenile barnacle. This involved tissue necrosis and regeneration in the fire coral host, leading to a callus ring structure around the juvenile barnacle, enhancing survival rate after settlement. The complex exploratory and settlement patterns and interactions documented here represent a breakthrough in coral reef symbiosis studies to show how invertebrates start symbiosis with fire corals.
  14. Axelsson EP, Abin JV, T Lardizabal ML, Ilstedt U, Grady KC
    Ecol Evol, 2022 May;12(5):e8855.
    PMID: 35509611 DOI: 10.1002/ece3.8855
    While reforestation is gaining momentum to moderate climate change via carbon sequestration, there is also an opportunity to use tree planting to confront declining global biodiversity. Where tree species vary in support of diversity, selecting appropriate species for planting could increase conservation effectiveness. We used a common garden experiment in Borneo using 24 native tree species to examine how variation among tree species in their support of beetle diversity is predicted by plant traits associated with "acquisitive" and "conservative" resource acquisition strategies. We evaluate three hypotheses: (1) beetle communities show fidelity to host identity as indicated by variation in abundance and diversity among tree species, (2) the leaf economic spectrum partially explains this variation as shown by beetle preferences for plant species that are predicted by plant traits, and (3) a small number of selected tree species can capture higher beetle species richness than a random tree species community. We found high variation among tree species in supporting three highly intercorrelated metrics of beetle communities: abundance, richness, and Shannon diversity. Variation in support of beetle communities was predicted by plant traits and varied by plant functional groups; within the dipterocarp family, high beetle diversity was predicted by conservative traits such as high wood density and slow growth, and in non-dipterocarps by the acquisitive traits of high foliar K and rapid growth. Using species accumulation curves and extrapolation to twice the original sample size, we show that 48 tree species were not enough to reach asymptote levels of beetle richness. Nevertheless, species accumulation curves of the six tree species with the highest richness had steeper slopes and supported 33% higher richness than a random community of tree species. Reforestation projects concerned about conservation can benefit by identifying tree species with a disproportional capacity to support biodiversity based on plant traits.
  15. Hirano Y, Kitayama K, Imai N
    Ecol Evol, 2022 Feb;12(3):e8669.
    PMID: 35309744 DOI: 10.1002/ece3.8669
    Soil organic phosphorus (P) compounds can be the main P source for plants in P-limited tropical rainforests. Phosphorus occurs in diverse chemical forms, including monoester P, diester P, and phytate, which require enzymatic hydrolysis by phosphatase into inorganic P before assimilation by plants. The interactions between plant interspecific differences in organic P acquisition strategies via phosphatase activities with root morphological traits would lead to P resource partitioning, but they have not been rigorously evaluated. We measured the activities of three classes of phosphatases (phosphomonoesterase, PME; phosphodiesterase, PDE; and phytase, PhT), specific root length (SRL), root diameter, and root tissue density in mature tree species with different mycorrhizal associations (ectomycorrhizal [ECM] or arbuscular mycorrhizal [AM]) and different successional status (climax or pioneer species) in Sabah, Malaysia. We studied nitrogen (N)- and P-fertilized plots to evaluate the acquisition strategies for organic P under P-limited conditions 7 years after fertilization was initiated. P fertilization reduced the PME activity in all studied species and reduced PhT and PDE activities more in climax species than in the two pioneer species, irrespective of the mycorrhizal type. PDE activity increased in some climax species after N fertilization, suggesting that these species allocate excess N to the synthesis of PDE. Moreover, PME and PhT activities, but not PDE activity, correlated positively with SRL. We suggest that climax species tend to be more strongly dependent on recalcitrant organic P (i.e., phytate and/or diester P) than pioneer species, regardless of the mycorrhizal type. We also suggest that trees in which root PME or PhT activity is enhanced can increase their SRL to acquire P efficiently. Resource partitioning of soil organic P would occur among species through differences in their phosphatase activities, which plays potentially ecologically important role in reducing the competition among coexisting tree species in lowland tropical rainforests.
  16. Hardenstine RS, He S, Cochran JEM, Braun CD, Cagua EF, Pierce SJ, et al.
    Ecol Evol, 2022 Jan;12(1):e8492.
    PMID: 35127024 DOI: 10.1002/ece3.8492
    The whale shark Rhincodon typus is found throughout the world's tropical and warm-temperate ocean basins. Despite their broad physical distribution, research on the species has been concentrated at a few aggregation sites. Comparing DNA sequences from sharks at different sites can provide a demographically neutral understanding of the whale shark's global ecology. Here, we created genetic profiles for 84 whale sharks from the Saudi Arabian Red Sea and 72 individuals from the coast of Tanzania using a combination of microsatellite and mitochondrial sequences. These two sites, separated by approximately 4500 km (shortest over-water distance), exhibit markedly different population demographics and behavioral ecologies. Eleven microsatellite DNA markers revealed that the two aggregation sites have similar levels of allelic richness and appear to be derived from the same source population. We sequenced the mitochondrial control region to produce multiple global haplotype networks (based on different alignment methodologies) that were broadly similar to each other in terms of population structure but suggested different demographic histories. Data from both microsatellite and mitochondrial markers demonstrated the stability of genetic diversity within the Saudi Arabian aggregation site throughout the sampling period. These results contrast previously measured declines in diversity at Ningaloo Reef, Western Australia. Mapping the geographic distribution of whale shark lineages provides insight into the species' connectivity and can be used to direct management efforts at both local and global scales. Similarly, understanding historical fluctuations in whale shark abundance provides a baseline by which to assess current trends. Continued development of new sequencing methods and the incorporation of genomic data could lead to considerable advances in the scientific understanding of whale shark population ecology and corresponding improvements to conservation policy.
  17. Guerrero-Sanchez S, Majewski K, Orozco-terWengel P, Saimin S, Goossens B
    Ecol Evol, 2022 Jan;12(1):e8531.
    PMID: 35127037 DOI: 10.1002/ece3.8531
    The Asian water monitor lizard, Varanus salvator, is one of the largest predators in Southeast Asia which persists in human-dominated landscapes and, as such, is a suitable model to understand the behavioral plasticity of generalists in anthropogenic landscapes. We used Local Convex Hull with adaptive algorithm to estimate the home range size of 14 GPS-tagged individuals, followed by a MAXENT approach and community prey composition to understand the habitat preferences within the landscape. We estimated larger home ranges in forest than in oil palm plantations, as well as a larger diversity and abundance of mammals. Core home ranges were always linked to water bodies. However, the use of underproductive oil palm, freshwater swamp forest, and degraded forest by monitor lizards were higher than other kind of vegetation. This suitable habitat is proportionally larger in forest (73.7%) than in oil palm plantations (39.6%). Generalized estimation equation models showed that, while full home range size was negatively associated with the abundance of mammals, core areas depicted a positive association with mammal abundance, as well as with the proportion of suitable habitat within the home range. Besides having smaller home ranges in oil palm plantations, our findings suggest that limited suitable habitat availability forces the Asian water monitor lizard's population to establish only one or very few core areas. Contrastingly, under the protection of forest, they have more core areas, widely dispersed within larger home ranges. We conclude that regardless the plasticity of the species, human-dominated landscapes are altering natural patterns of home range establishment in the monitor lizard's population, creating a potential ecological trap where conditions may not remain favorable for them in the long run. A deeper understanding of the ecological implications on the species and the prey community is advisable.
  18. Takeuchi Y, Ohtsuki H, Innan H
    Ecol Evol, 2022 Jan;12(1):e8462.
    PMID: 35136547 DOI: 10.1002/ece3.8462
    For community ecologists, "neutral or not?" is a fundamental question, and thus, rejecting neutrality is an important first step before investigating the deterministic processes underlying community dynamics. Hubbell's neutral model is an important contribution to the exploration of community dynamics, both technically and philosophically. However, the neutrality tests for this model are limited by a lack of statistical power, partly because the zero-sum assumption of the model is unrealistic. In this study, we developed a neutrality test for local communities that implements non-zero-sum community dynamics and determines the number of new species (N sp) between observations. For the non-zero-sum neutrality test, the model distributed the expected N sp, as calculated by extensive simulations, which allowed us to investigate the neutrality of the observed community by comparing the observed N sp with distributions of the expected N sp derived from the simulations. For this comparison, we developed a new "non-zero-sum N sp test," which we validated by running multiple neutral simulations using different parameter settings. We found that the non-zero-sum N sp test rejected neutrality at a near-significance level, which justified the validity of our approach. For an empirical test, the non-zero-sum N sp test was applied to real tropical tree communities in Panama and Malaysia. The non-zero-sum N sp test rejected neutrality in both communities when the observation interval was long and N sp was large. Hence, the non-zero-sum N sp test is an effective way to examine neutrality and has reasonable statistical power to reject the neutral model, especially when the observed N sp is large. This unique and simple approach is statistically powerful, even though it only employs two temporal sequences of community data. Thus, this test can be easily applied to existing datasets. In addition, application of the test will provide significant benefits for detecting changing biodiversity under climate change and anthropogenic disturbance.
  19. Abdul Aziz MF, Mohd Top Mohd Tah M, Shohaimi S, Ab Ghani NI, Fletcher C
    Ecol Evol, 2021 Aug;11(16):10741-10753.
    PMID: 34429877 DOI: 10.1002/ece3.7721
    A research study on morphometrics of Kalophrynus palmatissimus (commonly known as Lowland Grainy Frog) at Ayer Hitam Forest Reserve (AHFR), Selangor and Pasoh Forest Reserve (PFR), Negeri Sembilan was carried out from 12 November 2016 to 13 September 2017. The study was to examine data on the morphometric traits of K. palmatissimus at the two forest reserves. 15 morphometric traits of K. palmatissimus that were taken by using vernier calipers. Frog surveys were done by using 15 and 18 nocturnal 400 m transect lines with an interval distance of 20 m at AHFR and PFR, respectively. The GPS coordinates for all frog samples were recorded to ensure the precise geographic location. In addition, five climatic data were recorded. The results showed that most morphometric traits in AHFR (n = 34) and PFR (n = 31) were positively correlated with each other. On the other hand, climatic factor, which was soil pH, had a significant positive influence on most of the morphometric traits (p  .05). Later, it was found that the snout-vent length of K. palmatissimus at AHFR was slightly larger than at PFR (AHFR: μ = 37.00 mm, SE = 1.16 c.f. PFR: μ = 30.29 mm, SE = 1.07). It showed that there were variations in morphometric traits of K. palmatissimus at AHFR and PFR. From PCA analysis, morphometric traits are grouped into two components for AHFR and PFR, respectively. In AHFR, head length, eye diameter, head width, internarial distance, interorbital distance, forearm length, tibia length, foot length, and thigh length were strongly correlated, while snout length and eye-nostril distance were strongly correlated. In PFR, eye diameter, head width, internarial distance, interorbital distance, foot length, and thigh length were strongly correlated, though snout length and eye-nostril distance were strongly correlated, hence, suggested that all morphometric traits grow simultaneously in K. palmatissimus with eye-nostril distance (EN), and snout length (SL) growing almost simultaneously at AHFR (r = .91) and PFR (r = .97). There is still a lack of available information regarding the distribution and morphometric studies of K. palmatissimus in Malaysia, especially at AHFR and PFR. This study showed 15 different morphometric traits of K. palmatisssimus between AHFR and PFR, with K. palmatissimus at AHFR were found to be slightly larger than at PFR.
  20. Newbery DM, Stoll P
    Ecol Evol, 2021 Jun;11(11):6195-6222.
    PMID: 34141212 DOI: 10.1002/ece3.7452
    Classical tree neighborhood models use size variables acting at point distances. In a new approach here, trees were spatially extended as a function of their crown sizes, represented impressionistically as points within crown areas. Extension was accompanied by plasticity in the form of crown removal or relocation under the overlap of taller trees. Root systems were supposedly extended in a similar manner. For the 38 most abundant species in the focal size class (10-<100 cm stem girth) in two 4-ha plots at Danum (Sabah), for periods P1 (1986-1996) and P2 (1996-2007), stem growth rate and tree survival were individually regressed against stem size, and neighborhood conspecific (CON) and heterospecific (HET) basal areas within incremented steps in radius. Model parameters were critically assessed, and statistical robustness in the modeling was set by randomization testing. Classical and extended models differed importantly in their outcomes. Crown extension weakened the relationship of CON effect on growth versus plot species' abundance, showing that models without plasticity overestimated negative density dependence. A significant negative trend of difference in CON effects on growth (P2-P1) versus CON or HET effect on survival in P1 was strongest with crown extension. Model outcomes did not then support an explanation of CON and HET effects being due to (asymmetric) competition for light alone. An alternative hypothesis is that changes in CON effects on small trees, largely incurred by a drought phase (relaxing light limitation) in P2, and following the more shaded (suppressing) conditions in P1, were likely due to species-specific (symmetric) root competition and mycorrhizal processes. The very high variation in neighborhood composition and abundances led to a strong "neighborhood stochasticity" and hence to largely idiosyncratic species' responses. A need to much better understand the roles of rooting structure and processes at the individual tree level was highlighted.
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