cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12320111.v1
title: Closely related dinoflagellate species in vastly different habitats – an example of a marine–freshwater transition

description: Phytoplankton are present in a large variety of aquatic environments, ranging from small freshwater ponds to the oceans. Typically, freshwater and marine species are not closely related, indicating an ancient divergence and that salinity poses a strong dispersal barrier. Here we reveal a common recent origin of two dinoflagellates that are well adapted to different habitats. <i>Gymnodinium baicalense</i> inhabits the geologically old freshwater Lake Baikal, which is located in the middle of the Eurasian continent. <i>Gymnodinium corollarium</i>, on the other hand, is a brackish water species from the Baltic Sea. Both species form blooms under ice during the spring. We generated 10 DNA sequences from these species. The partial 28S rRNA gene from <i>G. baicalense</i> and the partial 18S rRNA gene and internal transcribed spacer-2 (ITS2) from <i>G. corollarium</i> were sequenced for the first time. A more detailed description of <i>G. baicalense</i>, which was previously known only from light microscopy observations, is also provided. In the laboratory we demonstrated that <i>G. baicalense</i> is strictly adapted to fresh water, while <i>G. corollarium</i> had a wide salinity tolerance. However, the two species have almost identical morphology, identical SSU rRNA gene sequences, and only small differences in the LSU rRNA gene and ITS2. We infer a common ancestor, which was a species from the Arctic region with a tolerance to a range of salinities. Our data support the scenario that the under-ice phytoplankton community in Lake Baikal has been formed recently, even though the lake is the oldest in the world.
DOI: 10.34740/kaggle/dsv/2262829
title: Herbarium 2021 RBS
DOI: 10.5281/zenodo.4746518
title: The evolutionary genomics of species' responses to climate change

description: This release includes the data and code that support the findings presented in: Aguirre-Liguori A, Ramírez-Barahona S, Gaut B. (2021) The evolutionary genomics of species' responses to climate change
DOI: 10.5281/zenodo.4746517
title: The evolutionary genomics of species' responses to climate change

description: This release includes the data and code that support the findings presented in: Aguirre-Liguori A, Ramírez-Barahona S, Gaut B. (2021) The evolutionary genomics of species' responses to climate change
DOI: 10.6084/m9.figshare.12853751
title: If a bird calls, will we detect it? Factors that can influence the detectability of calls on automated recording units in field conditions

description: Automated recording units (ARUs) are an integral instrument in a broad range of applications such as invasive species management, behavioural studies, and environmental impact assessments. They have become particularly important in conservation programmes for a range of cryptic threatened bird species. While the fundamental issues of signal attenuation and degradation are well known, understanding how environmental factors influence detectability of calls on ARU recordings in particular circumstances is essential for the accurate interpretation of their results. Using five transects spaced at equal angles running from a central playback source we tested the detectability of <i>Pezoporus flaviventris</i> (Western Ground Parrot) and <i>Atrichornis clamosus</i> (Noisy Scrub-bird) calls on Wildlife Acoustics SM2 and SM4 devices. Both species call from on or near the ground in moderately dense heathlands. Detectability of calls was affected by wind direction: fewer calls were detected on an ARU that was up-wind of the broadcast source compared with another on a down-wind unit. More calls were detected on ARUs deployed at higher relative elevation, and detectability decreased with increased distance from the playback source. Calls were detected at a greater distance from the playback source when using SM4 ARUs, compared to SM2 ARUs. Inconsistency in the detection of bird calls through space and time could lead to errors in metrics calculated from acoustic data. Further investigation is required to determine how environmental factors such as wind direction can be accounted for in data analysis.
DOI: 10.6084/m9.figshare.12853751.v2
title: If a bird calls, will we detect it? Factors that can influence the detectability of calls on automated recording units in field conditions

description: Automated recording units (ARUs) are an integral instrument in a broad range of applications such as invasive species management, behavioural studies, and environmental impact assessments. They have become particularly important in conservation programmes for a range of cryptic threatened bird species. While the fundamental issues of signal attenuation and degradation are well known, understanding how environmental factors influence detectability of calls on ARU recordings in particular circumstances is essential for the accurate interpretation of their results. Using five transects spaced at equal angles running from a central playback source we tested the detectability of <i>Pezoporus flaviventris</i> (Western Ground Parrot) and <i>Atrichornis clamosus</i> (Noisy Scrub-bird) calls on Wildlife Acoustics SM2 and SM4 devices. Both species call from on or near the ground in moderately dense heathlands. Detectability of calls was affected by wind direction: fewer calls were detected on an ARU that was up-wind of the broadcast source compared with another on a down-wind unit. More calls were detected on ARUs deployed at higher relative elevation, and detectability decreased with increased distance from the playback source. Calls were detected at a greater distance from the playback source when using SM4 ARUs, compared to SM2 ARUs. Inconsistency in the detection of bird calls through space and time could lead to errors in metrics calculated from acoustic data. Further investigation is required to determine how environmental factors such as wind direction can be accounted for in data analysis.
DOI: 10.6084/m9.figshare.12853751.v1
title: If a bird calls, will we detect it? Factors that can influence the detectability of calls on automated recording units in field conditions

description: Automated recording units (ARUs) are an integral instrument in a broad range of applications such as invasive species management, behavioural studies, and environmental impact assessments. They have become particularly important in conservation programmes for a range of cryptic threatened bird species. While the fundamental issues of signal attenuation and degradation are well known, understanding how environmental factors influence detectability of calls on ARU recordings in particular circumstances is essential for the accurate interpretation of their results. Using five transects spaced at equal angles running from a central playback source we tested the detectability of <i>Pezoporus flaviventris</i> (Western Ground Parrot) and <i>Atrichornis clamosus</i> (Noisy Scrub-bird) calls on Wildlife Acoustics SM2 and SM4 devices. Both species call from on or near the ground in moderately dense heathlands. Detectability of calls was affected by wind direction: fewer calls were detected on an ARU that was up-wind of the broadcast source compared with another on a down-wind unit. More calls were detected on ARUs deployed at higher relative elevation, and detectability decreased with increased distance from the playback source. Calls were detected at a greater distance from the playback source when using SM4 ARUs, compared to SM2 ARUs. Inconsistency in the detection of bird calls through space and time could lead to errors in metrics calculated from acoustic data. Further investigation is required to determine how environmental factors such as wind direction can be accounted for in data analysis.
DOI: 10.6084/m9.figshare.12853757
title: A taxonomic revision of the Striated Grasswren <i>Amytornis striatus</i> complex (Aves: Maluridae) after analysis of phylogenetic and phenotypic data

description: Taxonomy of the Striated Grasswren <i>Amytornis striatus</i> complex has long been contentious and remains incompletely resolved. Its many populations are distributed widely but disjunctly and show only subtle distinction in morphology and plumage. Genetic data are meagre and have not been correlated with phenotype. We conducted a phenotypic analysis across its range and obtained mitochondrial DNA sequences from most populations. We recognise three species: south-eastern Striated Grasswren <i>Amytornis striatus sensu stricto</i>, Opalton Grasswren <i>Amytornis rowleyi</i> in central Queensland and Rufous Grasswren <i>Amytornis whitei</i> in the remainder of the range, with subspecies in the Pilbara and in the central and western deserts. In <i>A. striatus</i> as so circumscribed, we separate allopatric Murray Mallee and central New South Wales populations subspecifically. Isolated populations of Rufous Grasswren, from the North West Cape Peninsula, Western Australia and Eyre Peninsula, South Australia are also distinct. Awareness of such unanticipated diversity within the group has profound implications for conservation.
DOI: 10.6084/m9.figshare.12853757.v1
title: A taxonomic revision of the Striated Grasswren <i>Amytornis striatus</i> complex (Aves: Maluridae) after analysis of phylogenetic and phenotypic data

description: Taxonomy of the Striated Grasswren <i>Amytornis striatus</i> complex has long been contentious and remains incompletely resolved. Its many populations are distributed widely but disjunctly and show only subtle distinction in morphology and plumage. Genetic data are meagre and have not been correlated with phenotype. We conducted a phenotypic analysis across its range and obtained mitochondrial DNA sequences from most populations. We recognise three species: south-eastern Striated Grasswren <i>Amytornis striatus sensu stricto</i>, Opalton Grasswren <i>Amytornis rowleyi</i> in central Queensland and Rufous Grasswren <i>Amytornis whitei</i> in the remainder of the range, with subspecies in the Pilbara and in the central and western deserts. In <i>A. striatus</i> as so circumscribed, we separate allopatric Murray Mallee and central New South Wales populations subspecifically. Isolated populations of Rufous Grasswren, from the North West Cape Peninsula, Western Australia and Eyre Peninsula, South Australia are also distinct. Awareness of such unanticipated diversity within the group has profound implications for conservation.
DOI: 10.6084/m9.figshare.12853748.v1
title: Improved systematics of lorikeets reflects their evolutionary history and frames conservation priorities

description: A well-supported genus-level classification of any group of organisms underpins downstream understanding of its evolutionary biology and enhances the role of phylogenetic diversity in guiding its conservation and management. The lorikeets (Psittaciformes: Loriini) are parrots for which genus-level systematics (phylogenetic relationships and classification) has long been unstable and unsatisfactory. Instability has manifested through frequently changing compositions of some genera (e.g. <i>Trichoglossus</i> and <i>Psitteuteles</i>). Other genera (e.g. <i>Charmosyna, Vini</i>) have become so large that their phenotypic heterogeneity alone at least questions whether they are monophyletic assemblages that genera should comprise. Recent molecular phylogenetic and phenotypic studies have improved the framework with which to rationalise genus-level systematics in lorikeets but some trenchant uncertainty has remained. Here we utilise published genomic data and tetrahedral analysis of plumage colour to develop a full review of the genus-level classification of lorikeets. Using existing phylogenetic relationships and a newly estimated time-calibrated tree for lorikeets, we show where paraphyletic assemblages have misled the classification of genera. We assign six species to three new genera and six other species to four previously described generic names that have been in synonymy in recent literature. Our taxonomic revision brings a new perspective informing and guiding the conservation and management of the lorikeets and their evolutionary biology.
DOI: 10.6084/m9.figshare.12853748
title: Improved systematics of lorikeets reflects their evolutionary history and frames conservation priorities

description: A well-supported genus-level classification of any group of organisms underpins downstream understanding of its evolutionary biology and enhances the role of phylogenetic diversity in guiding its conservation and management. The lorikeets (Psittaciformes: Loriini) are parrots for which genus-level systematics (phylogenetic relationships and classification) has long been unstable and unsatisfactory. Instability has manifested through frequently changing compositions of some genera (e.g. <i>Trichoglossus</i> and <i>Psitteuteles</i>). Other genera (e.g. <i>Charmosyna, Vini</i>) have become so large that their phenotypic heterogeneity alone at least questions whether they are monophyletic assemblages that genera should comprise. Recent molecular phylogenetic and phenotypic studies have improved the framework with which to rationalise genus-level systematics in lorikeets but some trenchant uncertainty has remained. Here we utilise published genomic data and tetrahedral analysis of plumage colour to develop a full review of the genus-level classification of lorikeets. Using existing phylogenetic relationships and a newly estimated time-calibrated tree for lorikeets, we show where paraphyletic assemblages have misled the classification of genera. We assign six species to three new genera and six other species to four previously described generic names that have been in synonymy in recent literature. Our taxonomic revision brings a new perspective informing and guiding the conservation and management of the lorikeets and their evolutionary biology.
DOI: 10.6084/m9.figshare.10317599.v1
title: More dead than alive: harvest for ceremonial headdresses threatens Pesquet’s Parrot in Papua New Guinea

description: The red feathers of Pesquet’s Parrot (<i>Psittrichas fulgidus)</i> are highly sought after for use in the headdresses of the highland cultures of Papuan New Guinea, however, it is unclear whether the harvest for headdresses represents a serious threat to the species’ survival. To quantify the potential impact of harvesting, we surveyed 170 people in Mingende of Kerowagi District, Chimbu Province, a locality well known for their use of Pesquet’s Parrot feathers. Of the survey respondents, 43% had headdresses containing Pesquet’s Parrot feathers, owning an average of 2.9 headdresses (± 2.4 SD, <i>N</i> = 69) with each contained 2.9 (± 1.9 SD, <i>N</i> = 35) Pesquet’s Parrots. We estimated that an average of 8.4 Pesquet’s Parrots are contained within each owner’s headdresses. Extrapolating for the adult population of Kerowagi District, via a bootstrap methodology, suggested that between ~160,000 ‒ 280,000 Pesquet’s Parrots may have been harvested for the headdresses present in this district alone. Our survey results suggest an annual purchase rate of 1.5% which equates to approximately 3,200 Pesquet’s Parrots being required annually for Kerowagi District alone. This is equivalent to ~8% of the estimated wild population. Given that the extant population is widely dispersed and highly mobile across areas of remote foothill forest, <i>in situ</i> conservation management is unlikely to be economically viable. However, given that a greater number of Pesquet’s Parrot exist in headdresses than are alive in the wild, we suggest that the most practical conservation intervention is to focus on prolonging the lifespan of existing headdresses.
DOI: 10.6084/m9.figshare.10317599
title: More dead than alive: harvest for ceremonial headdresses threatens Pesquet’s Parrot in Papua New Guinea

description: The red feathers of Pesquet’s Parrot (<i>Psittrichas fulgidus)</i> are highly sought after for use in the headdresses of the highland cultures of Papuan New Guinea, however, it is unclear whether the harvest for headdresses represents a serious threat to the species’ survival. To quantify the potential impact of harvesting, we surveyed 170 people in Mingende of Kerowagi District, Chimbu Province, a locality well known for their use of Pesquet’s Parrot feathers. Of the survey respondents, 43% had headdresses containing Pesquet’s Parrot feathers, owning an average of 2.9 headdresses (± 2.4 SD, <i>N</i> = 69) with each contained 2.9 (± 1.9 SD, <i>N</i> = 35) Pesquet’s Parrots. We estimated that an average of 8.4 Pesquet’s Parrots are contained within each owner’s headdresses. Extrapolating for the adult population of Kerowagi District, via a bootstrap methodology, suggested that between ~160,000 ‒ 280,000 Pesquet’s Parrots may have been harvested for the headdresses present in this district alone. Our survey results suggest an annual purchase rate of 1.5% which equates to approximately 3,200 Pesquet’s Parrots being required annually for Kerowagi District alone. This is equivalent to ~8% of the estimated wild population. Given that the extant population is widely dispersed and highly mobile across areas of remote foothill forest, <i>in situ</i> conservation management is unlikely to be economically viable. However, given that a greater number of Pesquet’s Parrot exist in headdresses than are alive in the wild, we suggest that the most practical conservation intervention is to focus on prolonging the lifespan of existing headdresses.
DOI: 10.6084/m9.figshare.12853742.v1
title: Native and exotic nest predators of Alwal (Golden-shouldered parrot <i>Psephotellus chrysopterygius)</i> on Olkola Country, Cape York Peninsula, Australia

description: Nest predation is considered a major cause of population decline for the Endangered Alwal <i>Psephotellus chrysopterygius</i> (Golden-shouldered parrot) in Cape York Peninsula, Australia. Camera-traps were installed at 28 Alwal nests across two breeding seasons in four important refuges for the parrot, to confirm nest predator identities and their impact on nesting success. Nest predators were more common at Alwal nests prior to fledging. The feral cat <i>Felis catus</i> and yellow-spotted monitor <i>Varanus panoptes</i> were the most common predators detected at nests, but the Black-backed butcherbird <i>Cracticus mentalis</i>, Pied butcherbird <i>C. nigrogularis</i> and Brown goshawk <i>Acciptier fasciatus</i> were also documented predating nests. Predators were significantly more common at nests in the days prior to fledging, possibly due to increased nest site activity. Nest success was higher amongst denser vegetation, indicating that cover may inhibit detection of nests by predators, particularly at fledging time. As with many threatened species globally, further monitoring is needed to disentangle knowledge of Alwal nest predation, including refined nest-monitoring techniques to document elusive predation events.
DOI: 10.6084/m9.figshare.12853742
title: Native and exotic nest predators of Alwal (Golden-shouldered parrot <i>Psephotellus chrysopterygius)</i> on Olkola Country, Cape York Peninsula, Australia

description: Nest predation is considered a major cause of population decline for the Endangered Alwal <i>Psephotellus chrysopterygius</i> (Golden-shouldered parrot) in Cape York Peninsula, Australia. Camera-traps were installed at 28 Alwal nests across two breeding seasons in four important refuges for the parrot, to confirm nest predator identities and their impact on nesting success. Nest predators were more common at Alwal nests prior to fledging. The feral cat <i>Felis catus</i> and yellow-spotted monitor <i>Varanus panoptes</i> were the most common predators detected at nests, but the Black-backed butcherbird <i>Cracticus mentalis</i>, Pied butcherbird <i>C. nigrogularis</i> and Brown goshawk <i>Acciptier fasciatus</i> were also documented predating nests. Predators were significantly more common at nests in the days prior to fledging, possibly due to increased nest site activity. Nest success was higher amongst denser vegetation, indicating that cover may inhibit detection of nests by predators, particularly at fledging time. As with many threatened species globally, further monitoring is needed to disentangle knowledge of Alwal nest predation, including refined nest-monitoring techniques to document elusive predation events.
DOI: 10.6084/m9.figshare.12924289
title: Feeding profitability is associated with Glossy Black-cockatoo (<i>Calyptorhynchus lathami</i> ssp. <i>lathami</i>) feed tree selection

description: Habitat modification and destruction are known to be responsible for declines in avian taxa. Specialist species such as the vulnerable Glossy Black-cockatoo (<i>Calyptorhynchus lathami</i> ssp. <i>lathami</i>) are particularly at risk due to the limited number of <i>Casuarina</i> and <i>Allocasuarina</i> species on which they feed, which is compounded by their propensity for selecting only specific individual feed trees within patches. This study aims to address the lack of understanding surrounding Glossy Black-cockatoo feeding ecology in southeast Queensland, Australia, by examining determinants of tree selection for <i>Allocasuarina littoralis</i> and <i>A. torulosa</i>. We conducted surveys to identify feed and non-feed trees of both <i>Allocasuarina</i> species, and differences between the physical and chemical characteristics of trees, cones, and seeds were investigated. We found that larger trees were preferentially foraged, with nutritional profitability as the primary factor governing tree selection. Feed tree cones had higher seed number and seed mass, with seeds containing higher levels of fatty acids and nutrients than non-feed tree cones. We conclude that further research should aim to delineate the factors contributing to these differences, alongside determining appropriate management strategies to support viable feeding habitat, which is most likely comprised of mixed age patches, capable of maintaining mature trees offering sufficient nutrient reward.
DOI: 10.6084/m9.figshare.12924289.v1
title: Feeding profitability is associated with Glossy Black-cockatoo (<i>Calyptorhynchus lathami</i> ssp. <i>lathami</i>) feed tree selection

description: Habitat modification and destruction are known to be responsible for declines in avian taxa. Specialist species such as the vulnerable Glossy Black-cockatoo (<i>Calyptorhynchus lathami</i> ssp. <i>lathami</i>) are particularly at risk due to the limited number of <i>Casuarina</i> and <i>Allocasuarina</i> species on which they feed, which is compounded by their propensity for selecting only specific individual feed trees within patches. This study aims to address the lack of understanding surrounding Glossy Black-cockatoo feeding ecology in southeast Queensland, Australia, by examining determinants of tree selection for <i>Allocasuarina littoralis</i> and <i>A. torulosa</i>. We conducted surveys to identify feed and non-feed trees of both <i>Allocasuarina</i> species, and differences between the physical and chemical characteristics of trees, cones, and seeds were investigated. We found that larger trees were preferentially foraged, with nutritional profitability as the primary factor governing tree selection. Feed tree cones had higher seed number and seed mass, with seeds containing higher levels of fatty acids and nutrients than non-feed tree cones. We conclude that further research should aim to delineate the factors contributing to these differences, alongside determining appropriate management strategies to support viable feeding habitat, which is most likely comprised of mixed age patches, capable of maintaining mature trees offering sufficient nutrient reward.