Diversity — Open Access Journal of Biodiversity

DNA barcoding has resulted in the ‘discovery’ of a vast number of new species and subspecies. Assigning formal scientific names to these taxa remains a major challenge. Names sometimes are newly designated. Alternatively, available valid names can be resurrected from synonymy, based on barcode analyses together with classical taxonomic characters. For the most part, however, new putative species revealed by barcoding studies go undescribed. This situation is most often attributed to insufficient taxonomic expertise with the authors conducting the study, together with a critical lack of formally trained taxonomists. However, even with formal training, and additional supportive data from morphological, ecological or life history characters, other factors can arise that impede new species descriptions. In the present paper, several specific taxonomic challenges that have arisen from barcode analyses in two groups of skipper butterflies (Lepidoptera: Hesperiidae), the Sootywings (Pholisora catullus and P. mejicanus) and the Coyote Cloudywing (Achalarus toxeus) are highlighted and discussed. Both P. catullus and A. toxeus show relatively large intraspecific genetic divergences of barcodes (2–3%) which suggests the possibility of previously unrecognized cryptic speciation within each group. Some of the challenges to providing formal names and clarifying taxonomic status of these cryptic taxa could be largely overcome by (1) barcoding type specimens, (2) clarifying imprecise and often vague or suspect type localities, and (3) by conducting in-depth comparative studies on genitalic morphology. Full article

Coral reefs globally are impacted by natural and anthropogenic stressors that are compounded by climate change. Understanding past reef responses to natural stressors (cyclones, sea-level change, freshwater inputs, and sedimentation) can provide important insights to further understand recent (within the past century) trends in coral cover and diversity. Here we use a compilation of recently published data to investigate the Holocene development of five fringing reefs that are located on a cross-shelf transect on the central Great Barrier Reef, and that are exposed to varying degrees of natural and anthropogenic sedimentation, storm exposure, and Holocene sea-level change. Forty-two reef cores collected using a combination of manual percussion coring and hydraulic drilling techniques, were analysed and dated using uranium-thorium methods. The chronostratigraphic records of reef development established using 105 recently published radiometric ages and seven new uranium-thorium ages from the reef cores and fossil microatolls preserved across the reef flats were compared to investigate cross-shelf variations in reef development. This is the first study to conduct an internal investigation of reef framework across an inshore–offshore gradient to examine the varying levels of influence of sedimentation, sea level and cyclones. Our observations from the central Great Barrier Reef show that reefs furthest offshore from the mainland coast were typically initiated earliest after the post-glacial marine transgression. Reef flat size, morphology, and growth style varied according to constraints placed on reef development by the composition, depth, shape, and relief of the underlying substrate. We establish that terrigenous sedimentation had a marked effect on the development of inshore reefs closest to the mainland (within 10 km of the mainland coast). Periods of relatively high terrigenous sedimentation correspond with enhanced reef accretion rates, and also resulted in a superior record of palaeo-ecological coral composition (i.e., better preservation) at inshore sites. In contrast, mid-Holocene cyclones played a seemingly more important role in the development of reefs >10 km from the mainland; although cyclones clearly affect reefs closer inshore, their geomorphology is affected by a range of controlling factors. Insights provided by these five Holocene reef chronostratigraphies provide useful baseline understanding of reef condition and growth along a cross-shelf transect where the reefs are exposed to variable stressors. Full article

The rich plant diversity that characterizes the West African Region and the inherent knowledge of their flora and vegetation has been the backbone of scientific explorations during the past centuries. The evolution of botanical knowledge on Guinea-Bissau, throughout the 16th and 20th centuries is reviewed. We present and discuss floristic data collected by scientific expeditions between the mid-1700s to 1974, when the Portuguese colonial period ended. Expeditions undertaken by French naturalists provided some of the earliest plant collections. A list of herbarium specimens collected by the French naturalist Jardin, in the Bijagós Islands in ca. 1847–1858 is presented here for the first time, while in the late 1800s some Portuguese naturalists also explored Guinea-Bissau. During the colonial period (1915–1974), Gomes e Sousa published the first comprehensive study of the territory’s flora while Espírito Santo assembled the largest plant collection. Our review applies a multi-disciplinary perspective to fill important lacuna regarding biodiversity knowledge of this under-researched West African country. It constitutes the first study tracing the long term evolution of knowledge on Guinea Bissau's plant diversity, which provides the basis for understanding trends and research priorities, in particular in conservation and botanical fields. Full article

The arid south Okanagan River Valley, British Columbia is a highly-modified landscape; where wetland and riparian habitat loss exceeds 85%, and 88% of remaining wetlands experience at least one harmful anthropogenic stressor. This multi-stressor landscape for amphibian species at risk led to a collaborative stakeholder approach for habitat restoration and species recovery. The main project goal was to increase the quantity and quality of lowland wetland habitat by reconnecting known amphibian-breeding sites with constructed and/or enhanced small ponds. Long-term amphibian monitoring data were used to determine strategic locations for wetland construction and/or enhancement. Habitat enhancement outcomes (N_total = 21 sites) since 2006 include 10 newly constructed ponds, enhancement of eight re-contoured ponds after historic infilling, and invasive predatory species removal at three sites. Project ponds were monitored annually (2007 to 2014) for calling frogs, the presence of eggs, and metamorphic emergence. Early signs of colonization and metamorphic success for Great Basin Spadefoot (Spea intermontana) (N = 13 sites) and Pacific treefrog (Pseudacris regilla) (N = 7 sites) populations have been observed, however no records of Blotched tiger salamanders (Ambystoma mavortium) colonization has been detected. Wetland habitat construction and enhancement have doubled the number of available fishless ponds to support breeding within the study area and engaged landowners through voluntary stewardship. Whether constructed or enhanced ponds have aided species recovery is unclear, though the colonization and successful metamorphosis of some species provides early supporting evidence that it will. Full article

In the current study, we present the molecular characterization of an endophyte fungus associated with the leaves of Deschampsia antarctica Desv. (Poaceae), a monocot species native to Antarctica. The isolate was obtained from 90 leaf fragments from two distinct collection sites, both located on Half Moon Island, South Shetland Islands and Maritime Antarctica. The internal transcribed spacer region (ITS) was sequenced and the endophytic fungus was identified as belonging to the genus Juncaceicola Tennakoon, Camporesi, Phook and K.D. Hyde (99% nucleotide sequence identity). When compared to all fungi of the genus Juncaceicola deposited in data base, our isolate showed greater proximity with Juncaceicola typharum, however, because it presents a low bootstrap value to be considered a new species, we treat it as Juncaceicola cf. typharum. Moreover, the identification of our isolate as belonging to the genus Juncaceicola makes this the first occurrence of a species of this genus to be associated with the leaves of Antarctic plants. This work is considered as a starting point for other studies with fungi of this genus associated with leaves of Deschampsia antarctica, as it presents results from two collection points on a single Antarctic island, suggesting that new sites and new Antarctic islands should be explored. Full article

Campomanesia adamantium is an endemic plant of Cerrado biome that has potential for cultivation because its fruits have culinary and medicinal uses. However, genetic diversity studies using molecular markers with Cerrado species are scarce, and the inadequate extractive exploitation of fruits and the expansion of agricultural frontiers may also affect genetic variability. Therefore, studies in this field are of interest as they can provide sources for conservation and breeding programs. In this context, we investigated the genetic diversity of native populations of C. adamantium from different sites and the relationship between genetic variability and the land use and land cover of each site. A total of 207 plants were sampled in seven sites and characterized with seven polymorphic microsatellite markers. The use and coverage of land were mapped based on aerial images, and the land was classified into different categories. The genetic diversity was high in all populations, with low levels of differentiation due to allele sharing, mainly in Mato Grosso do Sul and Paraguay populations. The geographically closest populations were more genetically similar. The use and coverage of land indicated that intense agriculture promotes a significant decrease in genetic variability. Full article

The winter roost of the long-eared owl Asiootus in Crimea (South of Ukraine), located in Simferopol, is described. In 2015–2017, the number of long-eared owls varied on a convex curve, with the maximum reached at the end of November and in December. The birds exhibited a strong preference for roosting in conifers, where we recorded 89% of the owls. There was an inverse relationship between the mean of the maximum daily temperature (°C) and the number of owls in both seasons. The owls were not sensitive to abrupt but short-term temperature changes, but the temperature decrease curve caused practically synchronous changes in the dynamics of bird numbers. It was found that the number of owls significantly differed based on weather conditions in 16 trees. The proportion of owls sitting on coniferous trees increased with unfavourable weather, and the converse pattern was observed for deciduous trees. Full article

Despite the rapid advancements in the field of road ecology, very little research has been done in railway ecology. Basic research, such as railway use by wildlife, is relatively undocumented, albeit very important in understanding the potential negative and positive effects of railways on wildlife and ecosystems. We provide one of the first studies documenting wildlife railway use using motion-triggered cameras along a 20 km stretch of railway in Ontario. Our objectives were to develop a much-needed baseline understanding of railway use by endemic wildlife species, investigate differences in frequency of use among species, compare diurnal versus nocturnal use, and determine if railway use by wildlife was uniform or spatially varied. We found a significant proportion of medium-to-large resident mammalian fauna and several avian species non-uniformly using the studied railway. Some species used the railway as a travel corridor, while others appeared to use it incidentally. Diel and seasonal patterns of use were apparent for many species. Our findings emphasize the importance of species-specific investigations of railway ecology. The collection of baseline information on railway use by wildlife is critical in view of the dearth of available data, and we highly encourage further research in all aspects of wildlife–railway ecology. Full article

Kgalagadi Transfrontier Park is located in northwestern South Africa and extends northeastward into Botswana. The park lies largely within the southern Kalahari Desert ecosystem where the Auob and Nassob rivers reach their confluence. Although these rivers run only about once every 100 years, or shortly after large thunderstorms, underground flows and seeps provide consistent surface water for the parks sparse vegetation and diverse wildlife. No formal studies on bats have previously occurred at Kgalagadi. We used SM2 + BAT ultrasonic detectors to survey 10 sites along the Auob and Nassob rivers from 5–16 April 2016. The units recorded 3960 call sequences that were analyzed using Kaleidoscope software for South African bats as well as visual determinations based on call structure attributes (low frequency, characteristic frequency, call duration, and bandwidth). We identified 12 species from four families: Rhinolophidae: Rhinolophus fumigatus. Molossidae: Chaerephon pumilus, and Sauromys petrophilus, Tadarida aegyptiaca; Miniopteridae: Miniopteris schreibersi (natalensis), Vespertilionidae: Laephotis botswanae, Myotis tricolor, Neoromicia capensis, N. nana, Pipistrellus hesperidus, Scotophilus dinganii, and S. viridus. The most abundant species during the survey period was N. capensis. We also used paired-site design to test for greater bat activity at water sources compared to dry sites, with dry sites being significantly more active. We conclude that species richness is much higher than previously known from this region and that more species may be present during the warmer months of the year. In addition, activity of bats during the dry season in Kgalagadi would likely be more concentrated around drinking opportunities, thus allowing for better detection of species richness in the area. Full article

Pteropus griseus (gray flying fox) is a species of Old World fruit bat that is listed by the International Union for Conservation of Nature (IUCN) as Data Deficient. The species is found on small islands in the Lesser Sundas and Sulawesi, and is endemic to Indonesia, but no contemporary roosts are known, and the last study of the species was in Timor in the Lesser Sundas. In this study, we describe the first known day roost in Sulawesi for Pteropus griseus and collected anecdotal evidence regarding conservation threats to the colony. We compared data from flying foxes collected from this roost to other P. griseus specimens and those of closely related co-occurring species to confirm its identity. We confirmed that this roost is likely of Pteropus griseus, though the subspecies identity remains to be determined. However, it is newly threatened by middlemen traders of bat meat from North Sulawesi arriving to encourage local villagers near the roost to hunt the bats. Elevated levels of hunting may deplete the entire colony in a single season should no conservation action be taken to safeguard the roost. Full article

This tribute commemorates the life and work of Guillermo (Willy) Kuschel, who made substantial contributions to the understanding of weevil systematics, evolution and biology. Willy was born in Chile in 1918 and studied philosophy, theology and biology. He became fascinated by weevils early on and completed his Ph.D. degree on South American Erirhinini. Subsequent employment by the University of Chile provided him with many opportunities to further his weevil research and undertake numerous collecting expeditions, including to remote and rugged locations such as the Juan Fernandez Islands and southern Chile. In 1963 he accepted a position at the Department of Scientific and Industrial Research in New Zealand, where he became Head of the Systematics Group in the Entomology Division. His emphasis on field work and collections led to the establishment of the New Zealand Arthropod Collection, which he guided through its greatest period of expansion. His retirement in 1983 offered him increased opportunities to pursue his weevil research. In 1988 he presented a new scheme of the higher classification of weevils, which ignited and inspired much subsequent research into weevil systematics. The breadth and quality of his research and his huge collecting efforts have left a legacy that will benefit future entomologists, especially weevil workers, for decades to come. This tribute presents a biography of Willy and accounts of his contributions to, and impact on, the systematics of weevils both regionally and globally. All of his publications and the genera and species named after him are listed in two appendices. Full article

Knowing how adaptation shapes morphological evolution is fundamental to understanding the processes that promote biological diversity. However, there is a lack of empirical evidence on the effects of adaptive radiations on phenotypic diversity, which is related to processes that promote phenotypic divergence and convergence. We applied comparative methods to identify shifts in adaptive peaks and to detect divergence and convergence in skull morphology of frugivorous bats (Phyllostomidae: Stenodermatinae and Carollinae), an ecologically diverse group with strong association between skull morphology, feeding performance and diet that suggests adaptive diversification through morphological innovation. We found divergence and convergence for skull morphology. Fifteen peak shifts were found for jaws, which result in four convergent and four divergent regimes. For skull, nine peak shifts were detected that result in three convergent and three divergent regimes. Furthermore, convergence was significant and strong for skull morphology since distantly related organisms converged to the same adaptive optima. Results suggest that convergence indicates the effect of restriction on phenotypes to keep the advantages provided by the skull phenotype that played a central role in the evolution of strict frugivory in phyllostomids. We conclude that convergence has limited phenotypic diversity of functional traits related to feeding in phyllostomid frugivores. Full article

There is increasing evidence of poleward migration of a broad range of taxa under the influence of a warming ocean. However, patchy research effort, the lack of pre-existing baseline data, and taxonomic uncertainty for some taxa means that unambiguous interpretation of observations is often difficult. Here, we propose that heterobranch sea slugs provide a useful target group for monitoring shifts in distribution. As many sea slugs are highly colourful, popular with underwater photographers and rock-pool ramblers, and found in accessible habitats, they provide an ideal target for citizen scientist programs, such as the Sea Slug Census. This maximises our ability to rapidly gain usable diversity and distributional data. Here, we review records of recent range extensions by tropical species into the subtropical and temperate waters of eastern Australia and document, for the first time in Australian waters, observations of three tropical species of sea slug as well as range extensions for a further six to various locations in the Tasman Sea. Full article

Oregano (Origanum vulgare L.) is a flowering plant that belongs to the mint family (Lamiaceae). It is used as a culinary herb and is often commercialized as a fine powder or a mixture of small fragments of dried leaves, which makes morphological recognition difficult. Like other commercial preparations of drugs and spices, the contamination of oregano mixtures with vegetable matter of lower quality, or the use of generic misleading names, are frequent and stress the need to develop a molecular traceability system to easily, quickly, and cheaply unveil these scams. The DNA-based analytical approach known as cpDNA barcoding is particularly suited for fraud identification in crop plant species (fresh products and food derivatives), and it represents a promising traceability tool as an alternative or complement to traditional detection methods. In the present study, we used a combined approach based on both qualitative and quantitative cpDNA barcoding with end-point and real-time polymerase chain reaction (PCR) analyses to assess the type and degree of contamination in commercial batches of common oregano. In a preliminary qualitative screening, we amplified, cloned, and sequenced a number of universal trnH-psbA- and trnL-barcoded regions, to identify the main contaminants in the samples under investigation. On the basis of these findings, we then developed and validated a species-specific and sequence-targeted method of testing for the quantitative assessment of contaminants, using trnL gene intron assays. Surprisingly, the results obtained in our case study indicated an almost total absence of O. vulgare in the commercial batches analyzed, but a high presence of group I contaminants (Satureja pilosa Velen.), and a moderate presence of group II contaminants (Cistus lanidifer L./Cistus albidus). Full article

Global loss of biodiversity is occurring at an alarming rate and is a major issue in current times. Long-term studies offer the possibility to analyse changes in biodiversity and allow assessments of anthropogenic interventions in ecosystems. At present, various studies in most countries show partially strong declines of insect populations. Due to their role as a food source for many organisms it is assumed that declines of insect abundance might have effects on higher trophic levels like insectivorous birds. For reliable statements on relationships between food availability and population trends, systematic and extensive records of breeding birds are necessary. In this study, we analysed the changes in the range of species, biodiversity, and abundance of a breeding bird community over 43 years in a large nature conservation area in southwest Germany (“Lampertheimer Altrhein” near Mannheim). Since 1974, considerable changes in the spectrum of breeding birds have been found, but the overall biodiversity index did not change. Furthermore, 70% of the investigated species showed decreasing numbers of breeding bird territories, and the overall number of territories across species declined by more than 65%. A classification based on the main diet during the breeding period and habitat use revealed strong declines for insectivorous birds in the study area, especially in wetland and open cultivated landscapes. Full article

Dendropoma lebeche is a prosobranch gastropod belonging to the family Vermetidae, which calcifies its shell on hard substrates in dense aggregates, forming biogenic constructions along the western Mediterranean intertidal habitat. It is an important ecosystem engineer and, due to its ecological value, is protected by international convention. The aim of this study is to investigate the mollusc composition and diversity occurring within Spanish vermetid bioconstructions. During the late summer 2013, three distant sites along the Mediterranean coast of Spain were sampled by scraping off the vermetid shells to study their associated assemblages. A total of 600 molluscs were identified within the classes of Polyplacophora (four species), Gastropoda (35 spp.) and Bivalvia (18 spp.). Multivariate analyses revealed significant differences in composition and trophic diversity of mollusc assemblages among the three sites, highlighting a clear geographical gradient. Overall, both herbivores (grazers and deposit feeders) and omnivores were the quantitatively dominant trophic groups, while carnivores (predators and ectoparasites) were very scarce. Our results point out that mollusc assemblages associated with vermetid bioconstructions are rich and diversified, both in populations structure and trophic diversity, confirming the important role of vermetid gastropods as ecosystem engineers and biodiversity enhancers in shallow coastal waters. Full article

The Entiminae are broad-nosed weevils constituting the most diverse subfamily of Curculionidae, with over 50 tribes. We performed Bayesian and Maximum Parsimony combined phylogenetic analyses with the main objective of testing higher-level relationships and the naturalness of the major Neotropical and Southern South American (Patagonia and Andes) tribes, including some members from other regions. We compiled a data matrix of 67 terminal units with 63 Entiminae species, as well as four outgroup taxa from Cyclominae, by 3522 molecular (from nuclear 18S rDNA and 28S rDNA, and mitochondrial 16S rDNA and COI gene sequences) and 70 morphological characters. The resulting trees recover a clade Entiminae with a monophyletic Cylydrorhinini and Premnotrypes branching off early. The tree resulting from parsimony analysis shows a clade of Leptopiini from the Australian region and another clade including taxa mainly distributed in the Palaearctic and Neotropical regions, but in the Bayesian tree the South American and Australian Leptopiini are grouped together. The mainly Palaearctic Entiminae (e.g., Brachyderini, Laparocerini, Otiorhynchini, Peritelini, Polydrusini, Phyllobiini and Sciaphylini) form a subclade separated from Southern Hemisphere taxa. Among the latter, the well-supported Naupactini are the sister group of the South American Tanymecini, excluding Platyaspistes, herein transferred to Leptopiini (new placement). Another well-justified clade is Eustylini–Geonemini, which also includes the enigmatic Galapagonotus, and the genus Artipus, thus corroborating its recent exclusion from Naupactini. Full article

As global climate change causes population declines across numerous taxa, it becomes critical to understand the specific pathway by which climatic and anthropogenic factors influence population size. Water availability is a key environmental condition that links climate and humans to species response, especially for rare or threatened butterflies that are highly sensitive to changes in climate and the surrounding landscape. We use the wetland-dependent endangered St. Francis’ satyr butterfly (Neonympha mitchellii francisci) to test how changes in water availability affect population size via changes in host plant growth. We show that long-term declines in water availability are directly linked to a decline in host plant growth and contributed to a population decrease of 95% for St. Francis’ satyrs in the past decade, threatening the persistence of the species. Recent restoration work, which includes efforts to increase water availability via hardwood removal, has been successful in increasing population numbers. Many butterflies are broadly dependent on water availability and flow, and only by understanding the specific pathway that directly links water availability to species response can we make effective conservation plans to prepare for the altered water conditions of the future. Full article

Three new species of the small entimine genus Philetaerobius Marshall, 1923 from southern Africa are described, P. endroedyi sp. n., P. garibebi sp. n. and P. louwi sp. n., with bibliographic reference to fuller descriptions and illustrations in the recent paper by Borovec et al. (2018) published in the journal Diversity 10 (2), 30, in which the names were not made available under the rules of the International Code of Zoological Nomenclature dealing with electronic publication. A lectotype is also here designated for P. nidicola Marshall, 1923. Full article