bluuebunny/crossref_metadata_2025_split huggingface dataset:
Migration‐tracking integrated phylogeography supports long‐distance dispersal‐driven divergence for a migratory bird species in the Japanese archipelago
Authors: Aoki Daisuke , Sakamoto Haruna , Kitazawa Munehiro , Kryukov Alexey P. , Takagi Masaoki 
Published: May 2021

AbstractLong‐distance dispersal (LDD) outside a species' breeding range contributes to genetic divergence. Previous phylogeographic studies of migratory bird species have not discriminated LDD from vicariant speciation in their diversification process. We conducted an integrative phylogeographic approach to test the LDD hypothesis, which predicts that a Japanese migratory bird subspecies diverged from a population in the coastal region of the East China Sea (CRECS) via LDD over the East China Sea (ECS). Haplotype networks of both mitochondrial and nuclear genes of its three subspecies were reconstructed to examine whether the Japanese subspecies of the Brown Shrike (Lanius cristatus superciliosus) diverged from an ancestral CRECS population. A species distribution model (SDM) for the Japanese subspecies was constructed using bioclimatic variables under the maximum entropy algorithm. It was projected backwards to the climate of the last glacial maximum (LGM) to infer the candidate source area of colonization. A migratory route of L. c. superciliosus, which possibly reflects a candidate past colonization route, was tracked by light‐level geolocators. Molecular phylogenetic networks suggest that the Japanese subspecies diverged from a population in the CRECS and maintained anciently diverged haplotypes. The SDM inferred that the emerged continental shelf of the ECS and the present CRECS were suitable breeding areas for the Japanese subspecies during the LGM. A major migratory route for L. c. superciliosus was inferred between the CRECS and the Japanese archipelago across the ECS. Our integrative approach supported the LDD hypothesis for divergence of the Japanese subspecies of the Brown Shrike. Shrinkage of the ECS may have been responsible for successful population establishment, due to a sufficient number of migrants overshooting to the Japanese archipelago from the CRECS. Our framework provides a new phylogeographic scenario for this region. Discriminating LDD and vicariance models helps improve our understanding of the phylogeographic histories of migratory species.
The impact of aquaculture on the genetics and distribution of the onuphid annelid Diopatra biscayensis
Authors: Galaska Matthew P. , Wethey David S. , Arias Andrés , Dubois Stanislas F. , Halanych Kenneth M. , Woodin Sarah A. 
Published: May 2021

AbstractAimEvolutionary history of natural populations can be confounded by human intervention such as the case of decorator worm species Diopatra (Onuphidae), which have a history of being transported through anthropogenic activities. Because they build tubes and act as ecosystem engineers, they can have a large impact on the overall ecosystem in which they occur. One conspicuous member, Diopatra biscayensis, which was only described in 2012, has a fragmented distribution that includes the Bay of Biscay and the Normanno‐Breton Gulf in the English Channel. This study explores the origin of these worms in the Normanno‐Breton region, which has been debated to either be the result of a historic range contraction from a relic continuous population or a more recent introduction.LocationNortheastern Atlantic, the Bay of Biscay, and the Normanno‐Breton Gulf.MethodsWe utilized a RAD‐tag‐based SNP approach to create a reduced genomic data set to recover fine‐scale population structure and infer which hypothesis best describes the D. biscayensis biogeographic distribution. The reduced genomic data set was used to calculate standard genetic diversities and genetic differentiation statistics, and utilized various clustering analyses, including PCAs, DAPC, and admixture.ResultsClustering analyses were consistent with D. biscayensis as a single population spanning the Bay of Biscay to the Normanno‐Breton Gulf in the English Channel, although unexpected genetic substructure was recovered from Arcachon Bay, in the middle of its geographic range. Consistent with a hypothesized introduction, the isolated Sainte‐Anne locality in the Normanno‐Breton Gulf was recovered to be a subset of the diversity found in the rest of the Bay of Biscay.Main conclusionsThese results are congruent with previous simulations that did not support connectivity from the Bay of Biscay to the Normanno‐Breton Gulf by natural dispersal. These genomic findings, with support from previous climatic studies, further support the hypothesis that D. biscayensis phylogeographic connectivity is the result of introductions, likely through the regions’ rich shellfish aquaculture, and not of a historically held range contraction.
Home‐site fidelity and homing behavior of the big‐headed turtle Platysternon megacephalum
Authors: Xiao Fanrong , Bu Rongping , Lin Liu , Wang Jichao , Shi Haitao 
Published: May 2021

AbstractSite fidelity refers to the restriction of dispersal distance of an animal and its tendency to return to a stationary site. To our knowledge, the homing ability of freshwater turtles and their fidelity is reportedly very low in Asia. We examined mark–recapture data spanning a 4‐year period in Diaoluoshan National Nature Reserve, Hainan Province, China, to investigate the site fidelity and homing behavior of big‐headed turtles Platysternon megacephalum. A total of 11 big‐headed turtles were captured, and all individuals were used in this mark–recapture study. The site fidelity results showed that the adult big‐headed turtles (n = 4) had a 71.43% recapture rate in the original site after their release at the same site, whereas the juveniles (n = 1) showed lower recapture rates (0%). Moreover, the homing behavior results showed that the adults (n = 5) had an 83.33% homing rate after displacement. Adult big‐headed turtles were able to return to their initial capture sites (home) from 150 to 2,400 m away and precisely to their home sites from either upstream or downstream of their capture sites or even from other streams. However, none of the juveniles (n = 4) returned home, despite only being displaced 25–150 m away. These results indicated that the adult big‐headed turtles showed high fidelity to their home site and strong homing ability. In contrast, the juvenile turtles may show an opposite trend but further research is needed.
Multisource noninvasive genetics of brown bears (Ursus arctos) in Greece reveals a highly structured population and a new matrilineal contact zone in southern Europe
Authors: Pylidis Charilaos , Anijalg Peeter , Saarma Urmas , Dawson Deborah A. , Karaiskou Nikoleta , Butlin Roger , Mertzanis Yorgos , Giannakopoulos Alexios , Iliopoulos Yorgos , Krupa Andrew , Burke Terence A. 
Published: May 2021

AbstractIn human‐dominated landscapes, connectivity is crucial for maintaining demographically stable mammalian populations. Here, we provide a comprehensive noninvasive genetic study for the brown bear population in the Hellenic Peninsula. We analyze its population structuring and connectivity, estimate its population size throughout its distribution, and describe its phylogeography in detail for the first time. Our results, based on 150 multilocus genotypes and on 244‐bp sequences of the mtDNA control region, show the population is comprised by three highly differentiated genetic clusters, consistent with geographical populations of Pindos, Peristeri, and Rhodope. By detecting two male bears with Rhodopean ancestry in the western demes, we provide strong evidence for the ongoing genetic connectivity of the geographically fragmented eastern and western distributions, which suggests connectivity of the larger East Balkan and Pindos‐Dinara populations. Total effective population size (Ne) was estimated to be 199 individuals, and total combined population size (NC) was 499, with each cluster showing a relatively high level of genetic variability, suggesting that migration has been sufficient to counteract genetic erosion. The mtNDA results were congruent with the microsatellite data, and the three genetic clusters were matched predominantly with an equal number of mtDNA haplotypes that belong to the brown bear Western mitochondrial lineage (Clade 1), with two haplotypes being globally new and endemic. The detection of a fourth haplotype that belongs to the Eastern lineage (Clade 3a1) in three bears from the western distribution places the southernmost secondary contact zone between the Eastern and Western lineages in Greece and generates new hypotheses about postglacial maxima migration routes. This work indicates that the genetic composition and diversity of Europe's low‐latitude fringe population are the outcome of ancient and historical events and highlight its importance for the connectivity and long‐term persistence of the species in the Balkans.
Quantitative measures and 3D shell models reveal interactions between bands and their position on growing snail shells
Authors: Jackson Hannah J. , Larsson Jenny , Davison Angus 
Published: May 2021

AbstractThe nature of shell growth in gastropods is useful because it preserves the ontogeny of shape, colour, and banding patterns, making them an ideal system for understanding how inherited variation develops, is established and maintained within a population. However, qualitative scoring of inherited shell characters means there is a lack of knowledge regarding the mechanisms that control fine variation. Here, we combine empirical measures of quantitative variation and 3D modeling of shells to understand how bands are placed and interact. By comparing five‐banded Cepaea individuals to shells lacking individual bands, we show that individual band absence has minor but significant impacts upon the position of remaining bands, implying that the locus controlling band presence/absence mainly acts after position is established. Then, we show that the shell grows at a similar rate, except for the region below the lowermost band. This demonstrates that wider bands of Cepaea are not an artifact of greater shell growth on the lower shell; they begin wider and grow at the same rate as other bands. Finally, we show that 3D models of shell shape and banding pattern, inferred from 2D photos using ShellShaper software, are congruent with empirical measures. This work therefore establishes a method that may be used for comparative studies of quantitative banding variation in snail shells, extraction of growth parameters, and morphometrics. In the future, studies that link the banding phenotype to the network of shell matrix proteins involved in biomineralization and patterning may ultimately aid in understanding the diversity of shell forms found in molluscs.
Reproductive traits and population dynamics of benthic invertebrates indicate episodic recruitment patterns across an Arctic polar front
Authors: Reed Adam J. , Godbold Jasmin A. , Solan Martin , Grange Laura J. 
Published: May 2021

AbstractClimate‐induced changes in the ocean and sea ice environment of the Arctic are beginning to generate major and rapid changes in Arctic ecosystems, but the effects of directional forcing on the persistence and distribution of species remain poorly understood. Here, we examine the reproductive traits and population dynamics of the bivalve Astarte crenata and sea star Ctenodiscus crispatus across a north–south transect that intersects the polar front in the Barents Sea. Both species present large oocytes indicative of short pelagic or direct development that do not differ in size–frequency between 74.5 and 81.3º latitude. However, despite gametogenic maturity, we found low frequencies of certain size classes within populations that may indicate periodic recruitment failure. We suggest that recruitment of A. crenata could occur periodically when conditions are favorable, while populations of C. crispatus are characterized by episodic recruitment failures. Pyloric caeca indices in C. crispatus show that food uptake is greatest at, and north of, the polar front, providing credence to the view that interannual variations in the quantity and quality of primary production and its flux to the seafloor, linked to the variable extent and thickness of sea ice, are likely to be strong determinants of physiological fitness. Our findings provide evidence that the distribution and long‐term survival of species is not only a simple function of adaptive capacity to specific environmental changes, but will also be contingent on the frequency and occurrence of years where environmental conditions support reproduction and settlement.
Pleistocene climate fluctuations as the major driver of genetic diversity and distribution patterns of the Caspian green lizard, Lacerta strigata Eichwald, 1831
Authors: Saberi‐Pirooz Reihaneh , Rajabi‐Maham Hassan , Ahmadzadeh Faraham , Kiabi Bahram H. , Javidkar Mohammad , Carretero Miguel A. 
Published: May 2021

AbstractGreen lizards of the genus Lacerta have served as excellent models for studying the impact of Pleistocene climatic oscillations on genetic structures. The Caspian green lizard, Lacerta strigata, occupies various habitats across the Caucasus and the South Caspian Sea, with the Hyrcanian Forests and north of the Alborz Mountains forming the core of the range. This study aimed to re‐examine the phylogenetic relationships of L. strigata with other congeneric members and to assess the genetic structure and historical demography of the species. Furthermore, Species Distribution Models (SDMs) were performed to infer the species' potential habitat suitability and were then projected on climate scenarios reflecting current and past (6 ky and 21 ky before present) conditions. A total of 39 individuals collected from most of the distribution range, together with additional lacertid species sequences from the GenBank database, were examined using mtDNA (Cyt b and 12S ribosomal RNA) and nuclear (C‐mos and β‐fibrinogen) sequence data. Based on the phylogenetic analyses, L. strigata was found to be a sister taxon to all other members of the genus. The species included two main clades (regional western and eastern) that diverged in a period between the Early and Middle Pleistocene. Based on the BBM and S‐Diva analyses, both dispersal and vicariance events explained the phylogeographic structure of the species in the Hyrcanian Forests. The historical demographic analyses using Bayesian skyline plots showed a mild increase in the effective population size from about 120 Kya for the western regional clade. According to phylogeographic structures and SDMs evidence, as in other species within the region, it appears that the south of the Caspian Sea (Hyrcanian Forests), and the Alborz Mountains acted as multiple refugia during cold periods and promoted expansion outwards amid the warm periods. Overall, the results provided evidence that the genetic structure of the species has been influenced by the Pleistocene climatic fluctuations.
Latitudinal influence on gametogenesis and host–parasite ecology in a marine bivalve model
Authors: Mahony Kate E. , Lynch Sharon A. , Egerton Sian , Laffan Rebecca E. , Correia Simão , de Montaudouin Xavier , Mesmer‐Dudons Nathalie , Freitas Rosa , Culloty Sarah C. 
Published: May 2021

AbstractReproduction and parasites have significant impacts on marine animal populations globally. This study aimed to investigate the associative effects of host reproduction and a host–parasite interplay on a marine bivalve, along a geographic gradient of latitude. Cockles Cerastoderma edule were sampled from five European sites (54°N to 40°N), between April 2018 and October 2019. A histological survey provided data on trematode (metacercaria and sporocyst life stages), prevalence, and cockle stage of gametogenesis to assess the influence of a latitudinal gradient on both interplays. Sex ratios at the northernmost sites were skewed toward females, and spawning size was reduced at the lower latitudes. Trematode infection did not follow a latitudinal gradient. Localized site‐related drivers, namely seawater temperature, varied spatially, having an impact on cockle–trematode interactions. Spawning was related to elevated temperatures at all sites. Prolonged spawning occurred at southern latitudes, where seawater temperatures were warmer. Trematode prevalence and the impact of trematodes on gametogenesis were found to be spatially variable, but not latitudinally. Therefore, it is not possible to determine the likelihood of boom and bust events in cockles, based on the latitudinal location of a population. In terms of sublethal impacts, it appeared that energy was allocated to reproduction rather than somatic growth in southern populations, with less energy allocated to reproduction in the larger, northern cockles. The demonstrated spatial trend of energy allocation indicates the potential of a temporal trend of reduced cockle growth at northern sites, as a result of warming sea temperatures. This awareness of the spatially varying drivers of populations is crucial considering the potential for these drivers/inhibitors to be exacerbated in a changing marine environment.
Modeling vegetation greenness and its climate sensitivity with deep‐learning technology
Authors: Chen Zhiting , Liu Hongyan , Xu Chongyang , Wu Xiuchen , Liang Boyi , Cao Jing , Chen Deliang 
Published: May 2021

AbstractClimate sensitivity of vegetation has long been explored using statistical or process‐based models. However, great uncertainties still remain due to the methodologies’ deficiency in capturing the complex interactions between climate and vegetation. Here, we developed global gridded climate–vegetation models based on long short‐term memory (LSTM) network, which is a powerful deep‐learning algorithm for long‐time series modeling, to achieve accurate vegetation monitoring and investigate the complex relationship between climate and vegetation. We selected the normalized difference vegetation index (NDVI) that represents vegetation greenness as model outputs. The climate data (monthly temperature and precipitation) were used as inputs. We trained the networks with data from 1982 to 2003, and the data from 2004 to 2015 were used to validate the models. Error analysis and sensitivity analysis were performed to assess the model errors and investigate the sensitivity of global vegetation to climate change. Results show that models based on deep learning are very effective in simulating and predicting the vegetation greenness dynamics. For models training, the root mean square error (RMSE) is <0.01. Model validation also assure the accuracy of our models. Furthermore, sensitivity analysis of models revealed a spatial pattern of global vegetation to climate, which provides us a new way to investigate the climate sensitivity of vegetation. Our study suggests that it is a good way to integrate deep‐learning method to monitor the vegetation change under global change. In the future, we can explore more complex climatic and ecological systems with deep learning and coupling with certain physical process to better understand the nature.
Niche–trait relationships at individual and population level in three co‐occurring passerine species
Authors: Shaner Pei‐Jen L. , Chen Yin‐Kai , Hsu Yu‐Cheng 
Published: May 2021

AbstractThe niche variation hypothesis (NVH) predicts that populations with wider niches exhibit greater morphological variation through increased interindividual differences in both niche and morphology. In this study, we examined niche–trait relationships in three passerine species (Cyanoderma ruficeps, Sinosuthora webbiana, and Zosterops simplex). A total of 289 C. ruficeps from 7 sites, 259 S. webbiana from 8 sites, and 144 Z. simplex from 6 sites were sampled along an elevation gradient (0–2,700 m) in Taiwan from 2009 to 2017. We measured bill traits (length, width, and depth of bill) and body size traits (length of head, tarsus, and wing) of the birds, which were reduced to four principal components (bill PC1, bill PC2, body size PC1, and body size PC2). We collected feather tissues for stable carbon and nitrogen isotope analyses to quantify their isotope niche. We quantified interindividual differences in isotope space and trait space with four diversity metrics (divergence, dispersion, evenness, and uniqueness) and tested whether interindividual differences in isotope space and trait space are positively associated. We quantified population isotope niche width by Bayesian ellipse area and population morphological variation by variances of the PCs. The results showed that individual uniqueness in isotope niche and bill morphology (average closeness of individuals within the population isotope/trait space) were positively associated across three species. Furthermore, isotope niche width and bill PC1 (reflecting the size of bill) variation at population level were also positively associated across the three species, supporting the NVH. Of the three species, C. ruficeps and S. webbiana showed stronger support for the NVH than Z. simplex, possibly due to the latter having narrower elevational distribution and a more specialized, plant‐based diet. The diversity metrics represented different aspects of interindividual differences in niche/trait space, and for the passerines, individual uniqueness appeared to play an important role in their niche–trait dynamics.
Lethal interactions among forest‐grouse predators are numerous, motivated by hunger and carcasses, and their impacts determined by the demographic value of the victims
Authors: Waggershauser Cristian N. , Ruffino Lise , Kortland Kenny , Lambin Xavier 
Published: May 2021

AbstractNew vertebrate communities are emerging in Europe following the recovery of multiple native predators to highly anthropized landscapes where predator control is still prevalent. While the lack of reference points for these communities creates novel challenges for conservationists and wildlife managers, they also provide opportunities to further our understanding of species interactions. Despite a growing body of evidence, many aspects of interactions among predators remain poorly understood, impairing our ability to anticipate the effects of such changes in predator communities. Through a systematic literature review, we gathered all the available evidence concerning the existence, strength, and demographic impacts of lethal predator interactions among forest‐grouse predators in Europe. We found a highly interconnected predator community, with 44 pairwise lethal interactions among 12 taxa. Three of these resulted in some degree of population suppression of the victim, while another three did not. However, most interactions (38) have not been evaluated for population suppression. Additionally, we highlight how predators interact simultaneously with a large range of other predators and identified at least two further taxa possibly suppressed through the combined impacts of multiple predators. We propose that interactions causing demographic suppression are characterized by impacts on individuals with high survival elasticity and that they are motivated by food limitation and additionally, in mammals, by competition for carcasses. Predator interactions, and our still poor understanding of them, introduce large uncertainties to conservation actions based on the management of predator abundances, which should be carefully evaluated.