PeerJ Preprints: Biogeographyhttps://peerj.com/preprints/index.atom?journal=peerj&subject=500Biogeography articles published in PeerJ PreprintsIntegrated modeling of phylogenies, species traits, and environmental gradients to better predict biogeographic distributionshttps://peerj.com/preprints/280012019-09-302019-09-30John M HumphreysJames B ElsnerThomas H JaggerScott J Steppan
There is an acknowledged need to combine species distribution and macro-ecological models with phylogenetic information, particularly when biogeographic research incorporates multiple species, explores phenotypic traits, or is spatially dynamic. Our aim is to present a new approach to multi-species joint modeling that applies spatially explicit phylogenetic regression to simultaneously predict species occurrence probability and the geographic distribution of interspecific continuous morphological traits. We developed a multi-tiered Bayesian geostatistical model that incorporates a species phylogeny, morphometric traits, and environmental variables to jointly estimate traits and geographic distributions for six species of South American leaf-eared mice (genus: Phyllotis). Covariates are included with the model to control for genetic relatedness, specimen age, specimen sex, and repeated measures errors. To help gauge model performance, we compared our approach to predictions made using several other species distribution modeling applications. Our integrated modeling framework demonstrated improved accuracy over alternative species distribution modeling techniques as judged by model sensitivity, specificity, and the true skill statistic. The inclusion of trait-based covariates and model terms to account for genetic relatedness, repeated measures, and spatial error were determined important as judged by credible intervals and parsimony metrics. Species distribution models and trait-based approaches that do not account for spatial dependencies, phylogenetic relationships, or repeated measures sampling errors may produce parameter estimates with smaller uncertainty than is warranted and produce predictions with significant error. Our study offers tools to address spatially and phylogenetically structured species data and presents an approach to integrating biological comparative methods in biogeographic research.
There is an acknowledged need to combine species distribution and macro-ecological models with phylogenetic information, particularly when biogeographic research incorporates multiple species, explores phenotypic traits, or is spatially dynamic. Our aim is to present a new approach to multi-species joint modeling that applies spatially explicit phylogenetic regression to simultaneously predict species occurrence probability and the geographic distribution of interspecific continuous morphological traits. We developed a multi-tiered Bayesian geostatistical model that incorporates a species phylogeny, morphometric traits, and environmental variables to jointly estimate traits and geographic distributions for six species of South American leaf-eared mice (genus: Phyllotis). Covariates are included with the model to control for genetic relatedness, specimen age, specimen sex, and repeated measures errors. To help gauge model performance, we compared our approach to predictions made using several other species distribution modeling applications. Our integrated modeling framework demonstrated improved accuracy over alternative species distribution modeling techniques as judged by model sensitivity, specificity, and the true skill statistic. The inclusion of trait-based covariates and model terms to account for genetic relatedness, repeated measures, and spatial error were determined important as judged by credible intervals and parsimony metrics. Species distribution models and trait-based approaches that do not account for spatial dependencies, phylogenetic relationships, or repeated measures sampling errors may produce parameter estimates with smaller uncertainty than is warranted and produce predictions with significant error. Our study offers tools to address spatially and phylogenetically structured species data and presents an approach to integrating biological comparative methods in biogeographic research.Barnacle recruit density and size increase from high to middle intertidal elevations in wave-exposed habitats on the Atlantic coast of Nova Scotiahttps://peerj.com/preprints/279662019-09-172019-09-17Ricardo A Scrosati
Barnacle recruitment is often studied in rocky intertidal habitats due to the relevant role that barnacles can play in intertidal communities. In 2014, barnacle (Semibalanus balanoides) recruitment was measured at high elevations in wave-exposed intertidal habitats on the NW Atlantic coast in Nova Scotia, Canada. Values were considerably lower than previously reported for middle elevations in wave-exposed intertidal habitats on the NE Atlantic and NE Pacific coasts. To determine if such differences in recruitment may have resulted from elevation influences, I did a field experiment in 2019 in wave-exposed intertidal habitats in Nova Scotia to test the hypothesis that recruitment is higher at middle than at high elevations, based on known environmental differences between both elevation zones. Based on data from three locations spanning 158 km of the Nova Scotia coast, barnacle recruitment was, on average, nearly 200 % higher (and recruits were larger) at middle than at high elevations. However, even with this increase, barnacle recruitment on this NW Atlantic coast is still lower than for comparable habitats on the NE Atlantic and NE Pacific coasts, and also lower than previously reported for wave-exposed locations farther south on the NW Atlantic coast, in Maine, USA. Therefore, barnacle recruitment in wave-exposed intertidal environments in Nova Scotia appears to be only moderate relative to other shores. This difference in the supply of barnacle recruits might influence the intensity of interspecific interactions involving barnacles.
Barnacle recruitment is often studied in rocky intertidal habitats due to the relevant role that barnacles can play in intertidal communities. In 2014, barnacle (Semibalanus balanoides) recruitment was measured at high elevations in wave-exposed intertidal habitats on the NW Atlantic coast in Nova Scotia, Canada. Values were considerably lower than previously reported for middle elevations in wave-exposed intertidal habitats on the NE Atlantic and NE Pacific coasts. To determine if such differences in recruitment may have resulted from elevation influences, I did a field experiment in 2019 in wave-exposed intertidal habitats in Nova Scotia to test the hypothesis that recruitment is higher at middle than at high elevations, based on known environmental differences between both elevation zones. Based on data from three locations spanning 158 km of the Nova Scotia coast, barnacle recruitment was, on average, nearly 200 % higher (and recruits were larger) at middle than at high elevations. However, even with this increase, barnacle recruitment on this NW Atlantic coast is still lower than for comparable habitats on the NE Atlantic and NE Pacific coasts, and also lower than previously reported for wave-exposed locations farther south on the NW Atlantic coast, in Maine, USA. Therefore, barnacle recruitment in wave-exposed intertidal environments in Nova Scotia appears to be only moderate relative to other shores. This difference in the supply of barnacle recruits might influence the intensity of interspecific interactions involving barnacles.The occurrence of pharmaceutical waste in different parts of the world: A scoping reviewhttps://peerj.com/preprints/279512019-09-102019-09-10Kim Yun JinMuhammad Shahzad Aslam
Pharmaceutical waste in our ecosystem is the huge burden for our future generations, especially in developing countries. It can be in every place even in drinking water after water treatment. It was observed the presence of over the counter drugs such as ibuprofen, naproxen, acetaminophen and antibiotic such as sulfamethoxazole, trimethoprim, erythromycin the most in the environment. Among all result, Carbamazepine which is known to treat epilepsy was found the most in the environment when the results were compiled from different parts of the world due to its low biodegradable properties. The current article is focused on the occurrence of pharmaceutical waste in the last eight years (January 2010- July 2018) published research work.
Pharmaceutical waste in our ecosystem is the huge burden for our future generations, especially in developing countries. It can be in every place even in drinking water after water treatment. It was observed the presence of over the counter drugs such as ibuprofen, naproxen, acetaminophen and antibiotic such as sulfamethoxazole, trimethoprim, erythromycin the most in the environment. Among all result, Carbamazepine which is known to treat epilepsy was found the most in the environment when the results were compiled from different parts of the world due to its low biodegradable properties. The current article is focused on the occurrence of pharmaceutical waste in the last eight years (January 2010- July 2018) published research work.Late Toarcian marine gastropods from the Cleveland Basin, UK: systematics, palaeobiogeography and contribution to biotic recovery from the early Toarcian extinction eventhttps://peerj.com/preprints/279472019-09-092019-09-09Mariel FerrariCrispin TS LittleJed W Atkinson
As part of a study to evaluate the recovery from the early Toarcian extinction event in the Cleveland Basin, 477 new gastropod specimens were collected from mid-late Toarcian rocks of the Ravenscar section, North Yorkshire, UK. The gastropods were preserved in two modes: 1) specimens preserved with recrystallized shells, mainly in the Whitby Mudstone Formation, but also some in the Blea Wyke Sandstone Formation; 2) specimens preserved as external moulds in mineralized patches of shells in the Yellow Sandstone Member. The fossil assemblage comprised fifteen species, of which three are new: Katosira? bicarinata sp. nov., Turritelloidea stepheni sp. nov. and Striactaenonina elegans sp. nov. Four species are described in open nomenclature, as Tricarilda? sp. Jurilda sp., Cylindrobullina sp. and Cossmannina sp. The other species have previously been described: Coelodiscus minutus (Schübler in Zieten), Procerithium quadrilineatum (Römer), Pseudokatosira undulata (Benz in von Zieten), Palaeorissoina aff. acuminata (Gründel), Pietteia unicarinata (Hudleston), Globularia cf. canina (Hudleston), Striactaeonina cf. richterorum Schulbert & Nützel, Striactaenonina aff. tenuistriata (Hudleston) and Sulcoactaeon sedgvici (Phillips). Most of these species are the earliest records of their respective genera and show palaeobiogeographical connections with contemporary gastropod associations from other regions of Europe and South America. The taxonomic composition of the late Toarcian Cleveland Basin gastropod assemblage differs substantially from the faunas of the late Pliensbachian and early Toarcian Tenuicostatum Zone, showing the strong effect of the early Toarcian mass extinction event on the marine gastropod communities in the basin. Only a few gastropod species are shared between the late Toarcian faunas and the much more diverse Aalenian gastropod faunas in the Cleveland Basin, suggesting there was a facies control on gastropod occurrences at that time. This is also a potential explanation for the taxonomic differences between the late Toarcian gastropod faunas in the Cleveland Basin and those in France, and Northern and Southern Germany.
As part of a study to evaluate the recovery from the early Toarcian extinction event in the Cleveland Basin, 477 new gastropod specimens were collected from mid-late Toarcian rocks of the Ravenscar section, North Yorkshire, UK. The gastropods were preserved in two modes: 1) specimens preserved with recrystallized shells, mainly in the Whitby Mudstone Formation, but also some in the Blea Wyke Sandstone Formation; 2) specimens preserved as external moulds in mineralized patches of shells in the Yellow Sandstone Member. The fossil assemblage comprised fifteen species, of which three are new: Katosira? bicarinata sp. nov., Turritelloideastepheni sp. nov. and Striactaenoninaelegans sp. nov. Four species are described in open nomenclature, as Tricarilda? sp. Jurilda sp., Cylindrobullina sp. and Cossmannina sp. The other species have previously been described: Coelodiscus minutus (Schübler in Zieten), Procerithium quadrilineatum (Römer), Pseudokatosira undulata (Benz in von Zieten), Palaeorissoina aff. acuminata (Gründel), Pietteia unicarinata (Hudleston), Globularia cf. canina (Hudleston), Striactaeonina cf. richterorum Schulbert & Nützel, Striactaenonina aff. tenuistriata (Hudleston) and Sulcoactaeon sedgvici (Phillips). Most of these species are the earliest records of their respective genera and show palaeobiogeographical connections with contemporary gastropod associations from other regions of Europe and South America. The taxonomic composition of the late Toarcian Cleveland Basin gastropod assemblage differs substantially from the faunas of the late Pliensbachian and early Toarcian Tenuicostatum Zone, showing the strong effect of the early Toarcian mass extinction event on the marine gastropod communities in the basin. Only a few gastropod species are shared between the late Toarcian faunas and the much more diverse Aalenian gastropod faunas in the Cleveland Basin, suggesting there was a facies control on gastropod occurrences at that time. This is also a potential explanation for the taxonomic differences between the late Toarcian gastropod faunas in the Cleveland Basin and those in France, and Northern and Southern Germany.A preliminary bird list from Río Luis, Veraguas provides further insight into an avian suture zone in Caribbean Panamahttps://peerj.com/preprints/279402019-09-052019-09-05Jessica F McLaughlinJorge Luis GarzonOscar G Lopez Ch.Matthew J Miller
We present a preliminary list of birds collected on the Caribbean coast of the province of Veraguas, Panama. Here, we found birds not known from the area, instead they were believed to range limits ending either east or west of our collection site. These include: Cnipodectes subbrunneus, Juliamyia julie, Gymnopithys bicolor bicolor, Mionectes (oleagineus) affinis, and western phylospecies of Malacoptila panamensis and Xenops minutus. Our results reaffirm that the coast of Veraguas is an important suture zone between Mesoamerica and South America avifaunas along the Caribbean coast of Panama.
We present a preliminary list of birds collected on the Caribbean coast of the province of Veraguas, Panama. Here, we found birds not known from the area, instead they were believed to range limits ending either east or west of our collection site. These include: Cnipodectes subbrunneus, Juliamyia julie, Gymnopithys bicolor bicolor, Mionectes (oleagineus) affinis, and western phylospecies of Malacoptila panamensis and Xenops minutus. Our results reaffirm that the coast of Veraguas is an important suture zone between Mesoamerica and South America avifaunas along the Caribbean coast of Panama.Pristinity, degradation and landscaping: the three angles of human impact on islandshttps://peerj.com/preprints/277752019-08-252019-08-25Valentí Rull
This paper presents three extreme examples of the potential consequences of human settlement on oceanic and continental islands. The Neotropical Pantepui continental archipelago of sky islands is an example of pristinity, which is due to the almost inexistent human impact because of the remoteness and inaccessibility of these islands as well as the lack of natural resources to exploit. Easter Island is used to illustrate almost total landscape degradation by deforestation and the exhaustion of natural resources, which has transformed the island into badlands with no signs of recovery. The Azores Islands have been chosen to illustrate landscaping as, after initial postsettlement deforestation and extractive practices, a further transformative phase occurred consisting of creating an almost totally anthropogenic landscape with mostly exotic species. The paper describes in some detail the developments of each case and the historical context in which they took place using historical, archeological and paleoecological evidence. Many intermediate states are possible among these three extremes, which can be represented with a ternary diagram (the PDL diagram), which is useful for characterizing the state of each island or archipelago, in terms of human impact, and to inform conservation and restoration practices.
This paper presents three extreme examples of the potential consequences of human settlement on oceanic and continental islands. The Neotropical Pantepui continental archipelago of sky islands is an example of pristinity, which is due to the almost inexistent human impact because of the remoteness and inaccessibility of these islands as well as the lack of natural resources to exploit. Easter Island is used to illustrate almost total landscape degradation by deforestation and the exhaustion of natural resources, which has transformed the island into badlands with no signs of recovery. The Azores Islands have been chosen to illustrate landscaping as, after initial postsettlement deforestation and extractive practices, a further transformative phase occurred consisting of creating an almost totally anthropogenic landscape with mostly exotic species. The paper describes in some detail the developments of each case and the historical context in which they took place using historical, archeological and paleoecological evidence. Many intermediate states are possible among these three extremes, which can be represented with a ternary diagram (the PDL diagram), which is useful for characterizing the state of each island or archipelago, in terms of human impact, and to inform conservation and restoration practices.Complex landscape topography can facilitate local adaptation during a range shifthttps://peerj.com/preprints/278992019-08-142019-08-14Robert N. FittLesley T. Lancaster
Warming climates provide many species the opportunity to colonise newly-suitable regions at higher latitudes and elevations. Despite becoming warmer, higher latitudes and elevations nevertheless offer novel climatic challenges, such as greater thermal variability and altered frequency of weather events, and these challenges exert selection on expanding populations. However, high gene flow and genetic drift during the expansion phase may limit the degree to which species can adapt to novel climatic conditions at the range front. Here we examine how landscape topographic complexity influences the opportunity for local adaptation to novel conditions during a range shift. Using RAD-seq data, we investigated whether elevation, latitude, climatic niche differentiation, and gene flow across a complex landscape were associated with signatures of adaptation during recent range expansion of the damselfly Ischnura elegans in Northeast Scotland. Our data revealed two distinct routes of colonisation, with admixture between these routes resulting in increased heterozygosity and population density. Expansion rates, assessed as directional rates of gene flow, were greater between more climatically similar sites than between climatically divergent sites. Significant genetic structure and allelic turnover was found to emerge near the range front at sites characterised by high elevation, low directional gene flow, and high spatial differentiation in climate regimes. This predictive combination of factors suggests that landscape complexity may be a prerequisite for promoting differentiation of populations, and providing opportunities for local adaptation, during rapid or contemporary range shifts.
Warming climates provide many species the opportunity to colonise newly-suitable regions at higher latitudes and elevations. Despite becoming warmer, higher latitudes and elevations nevertheless offer novel climatic challenges, such as greater thermal variability and altered frequency of weather events, and these challenges exert selection on expanding populations. However, high gene flow and genetic drift during the expansion phase may limit the degree to which species can adapt to novel climatic conditions at the range front. Here we examine how landscape topographic complexity influences the opportunity for local adaptation to novel conditions during a range shift. Using RAD-seq data, we investigated whether elevation, latitude, climatic niche differentiation, and gene flow across a complex landscape were associated with signatures of adaptation during recent range expansion of the damselfly Ischnura elegans in Northeast Scotland. Our data revealed two distinct routes of colonisation, with admixture between these routes resulting in increased heterozygosity and population density. Expansion rates, assessed as directional rates of gene flow, were greater between more climatically similar sites than between climatically divergent sites. Significant genetic structure and allelic turnover was found to emerge near the range front at sites characterised by high elevation, low directional gene flow, and high spatial differentiation in climate regimes. This predictive combination of factors suggests that landscape complexity may be a prerequisite for promoting differentiation of populations, and providing opportunities for local adaptation, during rapid or contemporary range shifts.Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asiahttps://peerj.com/preprints/278872019-08-082019-08-08Ze RenHongkai Gao
Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of bacterial community and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while fungal community and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams.
Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of bacterial community and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while fungal community and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams.No island-effect on stress for a rodent from a near-shore archipelagohttps://peerj.com/preprints/278302019-06-272019-06-27Nathan D StewartGabriela F MastromonacoGary Burness
Island rodents are often larger and live at higher population densities than their mainland counterparts, characteristics that have been referred to as “island syndrome”. Island syndrome has been well studied, but few studies have tested for island-mainland differences in stress physiology. We evaluated island syndrome within the context of stress physiology of white-footed mice (Peromyscus leucopus) captured from islands (n = 11) and mainland sites (n = 5) in Thousand Islands National Park, Ontario, Canada. Stress physiology was evaluated by quantifying corticosterone, the primary glucocorticoid (stress hormone) of rodents, from hair and its related metabolites from fecal samples. White-footed mice captured in this near-shore archipelago did not display characteristics of island syndrome, nor differences in levels of hair corticosterone or fecal corticosterone metabolites compared with mainland mice. We suggest that island white-footed mice experience similar degrees of stress in the Thousand Islands compared with the mainland. Although we did not find evidence of island syndrome or accompanying changes to stress physiology, we identified relationships between internal (sex, body mass) and external (season) factors and our hormonal indices of stress in white-footed mice.
Island rodents are often larger and live at higher population densities than their mainland counterparts, characteristics that have been referred to as “island syndrome”. Island syndrome has been well studied, but few studies have tested for island-mainland differences in stress physiology. We evaluated island syndrome within the context of stress physiology of white-footed mice (Peromyscus leucopus) captured from islands (n = 11) and mainland sites (n = 5) in Thousand Islands National Park, Ontario, Canada. Stress physiology was evaluated by quantifying corticosterone, the primary glucocorticoid (stress hormone) of rodents, from hair and its related metabolites from fecal samples. White-footed mice captured in this near-shore archipelago did not display characteristics of island syndrome, nor differences in levels of hair corticosterone or fecal corticosterone metabolites compared with mainland mice. We suggest that island white-footed mice experience similar degrees of stress in the Thousand Islands compared with the mainland. Although we did not find evidence of island syndrome or accompanying changes to stress physiology, we identified relationships between internal (sex, body mass) and external (season) factors and our hormonal indices of stress in white-footed mice.Polymorphisms and distribution of South American manatees (Trichechus spp.)https://peerj.com/preprints/277872019-06-062019-06-06Cibele Rodrigues BonvicinoMaria Carolina VianaEdivaldo HC de OliveiraRenata Emin-LimaJosé de Sousa e Silva JúniorMaura Elisabeth M SousaSalvatore Siciliano
Traditionally, the morphological attributes and the range of Trichechus species have been clearly established. However, we herein show that morphological traits, like belly and pectoral flipper coloration in South American manatees may be polymorphic. Karyotypic analysis of T. manatus allowed the precise identification of this species and confirmed the variability of the observed morphological findings. Molecular analysis based on cytochrome b DNA and the D-loop mitochondrial region showed shared haplotypes between T. inunguis and T. manatus, suggesting the presence of an ancestral polymorphism. These findings showed the need of improving the identification of these species before implementing conservation strategies. Finally, we present a complete report on the extant distribution of these species in South America.
Traditionally, the morphological attributes and the range of Trichechus species have been clearly established. However, we herein show that morphological traits, like belly and pectoral flipper coloration in South American manatees may be polymorphic. Karyotypic analysis of T. manatus allowed the precise identification of this species and confirmed the variability of the observed morphological findings. Molecular analysis based on cytochrome b DNA and the D-loop mitochondrial region showed shared haplotypes between T. inunguis and T. manatus, suggesting the presence of an ancestral polymorphism. These findings showed the need of improving the identification of these species before implementing conservation strategies. Finally, we present a complete report on the extant distribution of these species in South America.