Extant Populations Research Articles

Longitudinal characterization of the captive adult and tadpole Wyoming toad (Anaxyrus baxteri) microbiome

IntroductionAt one time thought to be extinct in the wild, the Wyoming toad (Anaxyrus baxteri) is one of the most critically endangered North American amphibian species. Despite approximately 20 years of ex situ breeding and reintroduction programs, this species remains functionally extinct in the wild. There is concern among those working in these programs that individuals bred in captivity fail to develop a microbiome that withstands the stressors of their native habitat following release. In related species, the skin microbiome has been shown to have a defensive function against common pathogens affecting these animals. However, the early-life microbiome of developing tadpoles in this species remains unknown and, therefore, this defensive function is unexplored in the Wyoming toad.MethodsThis study employed 16S rRNA amplicon sequencing to document the baseline microbiome of tadpole and adult Wyoming toads bred for release at Omaha’s Henry Doorly Zoo and Aquarium (Omaha, Nebraska, USA). We characterized the development of the mucosal microbiome in tadpoles and the mucosal and cloacal microbiome of adult toads.ResultsOur results revealed significant differences between tadpole and adult microbiomes, as well as significant sex-dependent differences within the adult Wyoming toads, in terms of richness and composition.DiscussionThese findings have identified the baseline microbiome of this endangered species and variables significantly influencing its composition in captivity. Ongoing studies of the only extant wild population are expected to identify taxa not found in captive toads, and potentially help 100 design husbandry modifications to maximize survivability following reintroduction to the wild.

Coupled social and ecological change drove the historical extinction of the California grizzly bear (Ursus arctos californicus).

Large carnivores (order Carnivora) are among the world's most threatened mammals due to a confluence of ecological and social forces that have unfolded over centuries. Combining specimens from natural history collections with documents from archival records, we reconstructed the factors surrounding the extinction of the California grizzly bear (Ursus arctos californicus), a once-abundant brown bear subspecies last seen in 1924. Historical documents portrayed California grizzlies as massive hypercarnivores that endangered public safety. Yet, morphological measurements on skulls and teeth generate smaller body size estimates in alignment with extant North American grizzly populations (approx. 200 kg). Stable isotope analysis (δ13C, δ15N) of pelts and bones (n = 57) revealed that grizzlies derived less than 10% of their nutrition from terrestrial animal sources and were therefore largely herbivorous for millennia prior to the first European arrival in this region in 1542. Later colonial land uses, beginning in 1769 with the Mission era, led grizzlies to moderately increase animal protein consumption (up to 26% of diet), but grizzlies still consumed far less livestock than otherwise claimed by contemporary accounts. We show how human activities can provoke short-term behavioural shifts, such as heightened levels of carnivory, that in turn can lead to exaggerated predation narratives and incentivize persecution, triggering rapid loss of an otherwise widespread and ecologically flexible animal.

Using resiliency, redundancy, and representation in a Bayesian belief network to assess imperilment of riverine fishes

AbstractConservation prioritization frameworks are used worldwide to identify species at greatest risk of extinction and to allocate limited resources across regions, species, and populations. Conservation prioritization can be impeded by ecological knowledge gaps and data deficiency, especially in freshwater species inhabiting highly complex aquatic ecosystems. Therefore, we developed a flexible approach that calculates a species' imperilment risk based on the conservation principles of resiliency, redundancy, and representation (i.e., the “three R's”). Our approach organizes data on species traits, distributions, population connectivity, and threats within a Bayesian belief network capable of predicting resiliency and redundancy within representative ecological settings. Empirical data and expert judgment inform the model to provide robust and repeatable risk assessments for rare and data‐deficient species. The model calculates resiliency at hierarchical spatial scales from distributional trends and population strength. Redundancy is estimated from the connectivity and quantities of extant populations. Resiliency, redundancy, and species' inherent vulnerability based on species traits collectively estimate extirpation risk within each unique ecological setting. Extirpation risks across ecological settings characterize representation and are aggregated to estimate global imperilment risk. We demonstrate the model's utility with Piebald Madtom (Noturus gladiator), a species petitioned for listing under the U.S. Endangered Species Act. Our results revealed that resiliency, redundancy, and extirpation risks can vary spatially across the species' range while identifying populations where additional sampling could disproportionally reduce uncertainty in estimated global imperilment risk. Our approach could standardize and expedite conservation status assessments, identify opportunities for early management intervention of at‐risk species and populations, and strategically reduce uncertainty by focusing monitoring and research on priority information gaps.

Multiclavula mucida (Basidiomycota) and other cryptogamic taxa in the Hungarian flora

The paper deals with the species found during cryptogamic flora mapping in 2023 that are remarkable from a floristic, taxonomic or conservational point of view. We present data from the Bükk Mts of two Trapeliopsis species which appear to be rare in Hungary. Multiclavula mucida, which is ap­parently a rare basidiomycete lichen species in Europe that prefers humid, montane habitats was dis­covered in the Mecsek Mts as a new species for the Hungarian flora. Of the knothole moss, Anacampto­don splachnoides, which is now thought to be entomophilic, we communicate the only extant popula­tion from Southern Transdanubia. We report the first occurrence of the atlantic-mediterranean Lepto­don smithii from the Hungarian side of the Great Hungarian Plain. Numerous data of the corticole Neck­era pennata indicate that in Hungary the distributional centre of this species is situated in the county of Baranya in the lowlands. New data from the Bükk Mts underline that in the Pannonian region Buxbaumia viridis is primarily a terricole species of acidophilous beech forests. We communicate the first occurrence from the lowlands of the alien lignicolous Sematophyllum adnatum which is danger­ous­ly spreading in Europe, at the same time one of the most vigorous populations in the Pannonian region. The third Hungarian occurrence of Callicladium haldanianum, a species that seems to spread in bogs, as well as the second occurrence of Racomitrium lanuginosum, growing abundantly on an ande­site boulder scree in Mátra Mts, are also reported here. Of Phegopteris connectilis we present in photo­graphic docu­mentation the first extant population from Southern Transdanubia, and we discuss whether the first publication from Mecsek Mts is correct or exact. In addition to listing the floristic data, we also briefly discuss the (mis)use of distribution data in the context of climate change, the difficulties of distinguish­ing the microtaxa of some pteridophytes, e.g. Asplenium adiantum-nigrum agg. and Dryop­teris affinis agg., and we correct one of our previously published, erroneous Hedwigia stellata data. Some interest­ing data of other taxa (such as Leucobryum glaucum, Palustriella commutata, Tetraphis pellucida, Gym­nocarpium robertianum, Ophioglossum vulgatum) are also mentioned in the paper.

The maternal genetic origin and diversity of the extant populations of the Ladakh region in India

Ladakh lies at a strategic location between the Indus River valley and the Hindu Khush Mountains, which makes the “Land of high passes” one of the major routes of movement. Through the years the region has faced multi-layered cultural movements, genetic assimilation and demographic changes. The initial settlement in the years goes back to the early Neolithic age and still continues despite its harsh, unhospitable and cold climate. Previous studies mostly covered the patrilineal markers of the region and an in-depth study lacked to represent the matrilineal ancestry and possible genetic inflow in the region. Hence, our current study first time generated complete mitogenomes of 108 unrelated individuals from Ladakh belonging to three population groups namely, Changpa (n = 38), Brokpa (n = 32) and Monpa (n = 38). In the in-depth analysis, we found that the mitogenome of the three Ladakhi groups are highly diverse in terms of maternal haplogroup distribution carrying lineages specific to East Asia (M9a), Tibbet (A21) and South Asia (M3, M30, U2). In our analysis we found that Changpa and Monpa probably have shared maternal ancestry compared to Brokpa, which is very distinct and also later suffered possible historical Bottleneck. Bayesian evolutionary and Network analysis indicates more ancient maternal lineage of Changpa and Monpa in terms of M9a haplotypes, but they also share some genetic history with Tibeto-Burman speakers in past. These findings conclusively indicate possible matrilineal genetic inflow in Ladakh from three directions, primarily from East Asia or South East Asia during post-glacial, West Eurasia and also from South Asia.

ADNA, ethnography, and facial approximations of the Teouma Lapita burials (c. 3000BP)

Although ancient DNA (aDNA) cannot predict the facial appearance of skeletal human remains, knowing which extant populations are most closely related to the deceased has proven to be invaluable in rectifying two early facial approximations (popularly known as facial reconstruction) undertaken 15 years ago. These concerned two of the crania excavated from the Lapita burial site at Teouma on the island of Efate, and are associated with the first human arrival in the Vanuatu archipelago approximately 3000 years ago. This experimental revision to incorporate aDNA into both the methods and results has found there are advantages of knowing the genetic affiliation for estimating facial appearance. Specifically, we have found that this knowledge (i) facilitates identifying which of the current statistically valid predictors of the facial features are the most appropriate, (ii) informs the depiction of sexually dimorphic patterns of facial aging, and (iii) guides the portrayal of the subtle facial morphologies that fall outside what is currently provided by statistically validated skull-soft tissue algorithms and inter-relationships.

Living on the edge: urban fireflies (Coleoptera, Lampyridae) in Morelia, Michoacán, Mexico.

Fireflies (Coleoptera, Lampyridae) are a globally threatened group of insects due to habitat loss and fragmentation, light pollution, climate change and pesticides. However, against all odds, some firefly populations persist in urbanized environments where all four of these factors are present simultaneously. In this work, we compiled several data sources to document the diversity of fireflies in the urbanized area of Morelia, characterize their current habitats, and determine the main stressors affecting these bioluminescent insects. We found seven genera and 26 species of fireflies (19 nocturnal, seven diurnal) associated with 32 urban, peri-urban and extra-urban areas; at least, 14 are new records for Michoacán, and the list for the state now includes nine genera and 41 species. Five additional sites were documented as extinction sites. We compared the characteristics of these five sites with those of the sites with extant populations. We found that in Morelia, fireflies are mainly associated with areas that have high to moderate proportions of vegetation cover, are near water bodies, have very gentle to moderate slopes, and are exposed to low levels of light pollution. In contrast, the extinction sites showed high proportions of artificial surfaces and high levels of light pollution. Because some fireflies are considered bioindicators of ecosystem integrity as they are associated to specific habitats, are highly diverse and due to their sensitivity to environmental changes, we consider that sites from Morelia's urban core and extinction sites show the highest levels of environmental degradation, threatening most fireflies and other insects living in the urban core with local extinction. At the same time, our results also suggest that implementing conservation strategies and sustainable planning for the urban development of Morelia in the short term could allow fireflies and other vital elements of the city's insect communities to persist for future generations. Restoration and conservation of green areas and nighttime environments are essential for biodiversity and human health, especially in intra-urban zones.

Multiclavula mucida (Basidiomycota) and other cryptogamic taxa in the Hungarian flora

The paper deals with the species found during cryptogamic flora mapping in 2023 that are remarkable from a floristic, taxonomic or conservational point of view. We present data from the Bükk Mts of two Trapeliopsis species which appear to be rare in Hungary. Multiclavula mucida, which is ap­parently a rare basidiomycete lichen species in Europe that prefers humid, montane habitats was dis­covered in the Mecsek Mts as a new species for the Hungarian flora. Of the knothole moss, Anacampto­don splachnoides, which is now thought to be entomophilic, we communicate the only extant popula­tion from Southern Transdanubia. We report the first occurrence of the atlantic-mediterranean Lepto­don smithii from the Hungarian side of the Great Hungarian Plain. Numerous data of the corticole Neck­era pennata indicate that in Hungary the distributional centre of this species is situated in the county of Baranya in the lowlands. New data from the Bükk Mts underline that in the Pannonian region Buxbaumia viridis is primarily a terricole species of acidophilous beech forests. We communicate the first occurrence from the lowlands of the alien lignicolous Sematophyllum adnatum which is danger­ous­ly spreading in Europe, at the same time one of the most vigorous populations in the Pannonian region. The third Hungarian occurrence of Callicladium haldanianum, a species that seems to spread in bogs, as well as the second occurrence of Racomitrium lanuginosum, growing abundantly on an ande­site boulder scree in Mátra Mts, are also reported here. Of Phegopteris connectilis we present in photo­graphic docu­mentation the first extant population from Southern Transdanubia, and we discuss whether the first publication from Mecsek Mts is correct or exact. In addition to listing the floristic data, we also briefly discuss the (mis)use of distribution data in the context of climate change, the difficulties of distinguish­ing the microtaxa of some pteridophytes, e.g. Asplenium adiantum-nigrum agg. and Dryop­teris affinis agg., and we correct one of our previously published, erroneous Hedwigia stellata data. Some interest­ing data of other taxa (such as Leucobryum glaucum, Palustriella commutata, Tetraphis pellucida, Gym­nocarpium robertianum, Ophioglossum vulgatum) are also mentioned in the paper.

The time and place of origin of South Caucasian languages: insights into past human societies, ecosystems and human population genetics

This study re-examines the linguistic phylogeny of the South Caucasian linguistic family (aka the Kartvelian linguistic family) and attempts to identify its Urheimat. We apply Bayesian phylogenetics to infer a dated phylogeny of the South Caucasian languages. We infer the Urheimat and the reasons for the split of the Kartvelian languages by taking into consideration (1) the past distribution ranges of wildlife elements whose names can be traced back to proto-Kartvelian roots, (2) the distribution ranges of past cultures and (3) the genetic variations of past and extant human populations. Our best-fit Bayesian phylogenetic model is in agreement with the widely accepted topology suggested by previous studies. However, in contrast to these studies, our model suggests earlier mean split dates, according to which the divergence between Svan and Karto-Zan occurred in the early Copper Age, while Georgian and Zan diverged in the early Iron Age. The split of Zan into Megrelian and Laz is widely attributed to the spread of Georgian and/or Georgian speakers in the seventh-eighth centuries CE. Our analyses place the Kartvelian Urheimat in an area that largely intersects the Colchis glacial refugium in the South Caucasus. The divergence of Kartvelian languages is strongly associated with differences in the rate of technological expansions in relation to landscape heterogeneity, as well as the emergence of state-run communities. Neolithic societies could not colonize dense forests, whereas Copper Age societies made limited progress in this regard, but not to the same degree of success achieved by Bronze and Iron Age societies. The paper also discusses the importance of glacial refugia in laying the foundation for linguistic families and where Indo-European languages might have originated.

Anopheles gambiae on remote islands in the Indian Ocean: origins and prospects for malaria elimination by genetic modification of extant populations

The mosquito Anopheles gambiae s.s. is a primary malaria vector throughout sub-Saharan Africa including the islands of the Comoros archipelago (Anjouan, Grande Comore, Mayotte and Mohéli). These islands are located at the northern end of the Mozambique Channel in eastern Africa. Previous studies have shown a relatively high degree of genetic isolation between the Comoros islands and mainland populations of A. gambiae, but the origin of the island populations remains unclear. Here, we analyzed phylogenetic relationships among island and mainland populations using complete mitochondrial genome sequences of individual A. gambiae specimens. This work augments earlier studies based on analysis of the nuclear genome. We investigated the source population of A. gambiae for each island, estimated the number of introductions, when they occurred and explored evidence for contemporary gene flow between island and mainland populations. These studies are relevant to understanding historical patterns in the dispersal of this important malaria vector and provide information critical to assessing their potential for the exploration of genetic-based vector control methods to eliminate this disease. Phylogenetic analysis and haplotype networks were constructed from mitogenome sequences of 258 A. gambiae from the four islands. In addition, 112 individuals from seven countries across sub-Saharan Africa and Madagascar were included to identify potential source populations. Our results suggest that introduction events of A. gambiae into the Comoros archipelago were rare and recent events and support earlier claims that gene flow between the mainland and these islands is limited. This study is concordant with earlier work suggesting the suitability of these oceanic islands as appropriate sites for conducting field trial releases of genetically engineered mosquitoes (GEMs).

The latest ancestor of extant raccoon-dog from Zhoukoudian, Beijing, China, highlights a complex or convoluted transition on the dietary habits

ABSTRACT There has always been a taxonomic controversy over the Middle Pleistocene raccoon-dogs, such as those from ZKD (=Zhoukoudian), which have previously been referred to either as Nyctereutes sinensis or N. procyonoides. Here, the specimens from ZKD Loc.1 and 13 have been re-evaluated and a number of diagnostic features have been identified and summarised. It is strongly recommended that they be classified as a new species, Nyctereutes peii, characterised by the robust dentition. The rationale and necessity for the establishment of N. peii has also been addressed from a number of perspectives. In addition, the evolution of the raccoon-dog’s foraging habits was outlined here for the first time using the molar ratio method. Surprisingly, the evolution of the foraging habits is not linear and gradual, but rather complex or tortuous. N. peii unexpectedly showed a less omnivorous habit than other populations. After that, however, there was a sudden reversal in the evolutionary trajectory, a major turning point in the evolution of the raccoon-dog that heralded the arrival of the extant population. Although the mechanism and dynamics are not fully understood and will need to be studied, the authors suggest that it may be linked to the dramatic fluctuations in global climate. LSID urn:lsid:zoobank.org:act:EF024839-3475-4249-902F-6E68D7A901BC

Is it time for genetic reinforcement of French Iberian ibex populations?

An evolutionary significant unit of the Iberian ibex (Capra pyrenaica), the Pyrenean ibex or “bucardo” (Capra pyrenaica pyrenaica) became extinct in its natural range, the Pyrenees, at the beginning of the twentieth-first century. Several years later (2014–2021) more than 250 specimens (C. p. victoriae) coming from the same donor population from central Spain were released in four localities of the French Pyrenees. Despite an initial fast demographic increase, the genetic variability of these populations remains low. Moreover, it is expected that genetic variability continues to decline due to genetic drift and that inbreeding accumulates. Here we revise options for genetic rescue or reinforcement of these populations involving future release of animals from different extant Spanish populations, mainly those belonging to the subpecies C. p. hispanica. The future hybridization between both phenotypes or “subspecies” may occur anyways in the next years, since currently there is a natural expansion of C. P. hispanica populations from the southern Pyrenees (Spanish side).

Bridging the extant and fossil record of planktonic foraminifera: implications for the Globigerina lineage

AbstractWe conducted a morphometric study and wall texture analysis on extant and fossil specimens of the planktonic foraminifera Globigerina falconensis plexus. Our global data reveal morphological inconsistencies between fossil and extant populations. Our results are significant as G. falconensis is widely used in palaeoceanographic studies in conjunction with its sister taxon G. bulloides. Morphologically these two species are similar, with the main difference being the distinctive apertural lip present in G. falconensis. We selected cores covering the entire stratigraphic range of G. falconensis, from the early Miocene to current day, spanning sites from high latitudes in the North Atlantic Ocean and the southern Indian Ocean to sites in equatorial regions. The morphology found in the modern ocean is not consistent with the Miocene holotype of Globigerina falconensis Blow described from lower Miocene sediments in Venezuela. A more lobate morphology evolved in the late Miocene, thus, a new name is required for this morphotype, coexisting in the modern oceans with G. falconensis s.s. We thus describe the new morphospecies, G. neofalconensis for the more lobate forms which evolved in the late Miocene and inhabit the modern oceans. Additionally, we report a pseudocancellate wall texture present in the G. falconensis plexus. We use the molecular sequences from the PR2 database to explore the generic attribution of the G. falconensis lineage, confirming its close relationship with G. bulloides and its retention in the genus Globigerina.

The maternal ancestry of the Kavaratti islanders and the last glacial maximum aftermath.

The prehistoric human settlement of the Lakshadweep islands remains a mystery for various reasons. Uncertainty about the existence of indigenous tribes in these islands and the lack of folklore records present major obstacles to the reconstruction of Lakshadweep ancestry. However, with extant population data, we seek to understand the maternal ancestry of theKavaratti islanders. Mitochondrial control region variation analysis of 80 individuals from this island shows maternal links with the populations in the northwestern region of the South Asian mainland. The founder clade R30b2, observed in the Kavaratti islanders, is so far present only in the Scheduled Castes from the Punjab region, Jat Sikhs and Nairs. All other mainland populations carry basal R30 or R30a subclades. The presence of a specific Uralic U4 lineage in our samples, in addition to the Indo-European affinity observed in the phylogeny tree, substantiates a northwestern maternal ancestry of the Kavaratti islanders and implies an ancestral admixture with early humans in the Near East at the time of the last glacial maximum (LGM). Based on our Bayesian analysis, we furthermore propose that a group bearing mostly R30b2 during the LGM recovery, moved eastward and southward, where they received Indian-specific M haplogroups. Hence, the maternal ancestry of the Kavaratti islanders is evidently a consequence of the demographic changes in the northwestern region of the Indian subcontinent caused by the Last Glacial Maximum. The haplogroup distribution pattern and nucleotide sequence data produced in this study will enrich the forensic database of the Lakshadweep islands.

Population genetics of Camellia granthamiana, an endangered plant species with extremely small populations in China.

Introduction: Camellia, the largest genus of Theaceae, is well-known for having high economic values. Camellia granthamiana demonstrates large beautiful flowers with some primitive characters, such as multiple large and persistent bracteoles and sepals, was listed as Vulnerable species on the IUCN Red List. Methods: In this study, we investigated all possible records of the species, and sampled four natural populations and five cultivated individuals. By applying shallow-genome sequencing for nine individuals and RAD-seq sequencing for all the sampled 77 individuals, we investigated population genetic diversity and population structure of the species. Results and discussion: The results showed that the population sampled from Fengkai, previously identified as C. albogigias, possessed different plastid genome from other species possibly due to plastid capture; the species possesses strong population structure possibly due to the effect of isolation by distance, habitat fragmentation, and self-crossing tendency of the species, whose effective population size declined quickly in the past 4,000 years. Nevertheless, C. granthamiana maintains a medium level of genetic diversity within population, and significant differentiation was observed among the four investigated populations, it is anticipated that more populations are expected to be found and all these extant populations should be taken into instant protection.

Comparing reintroduction strategies for the endangered San Francisco gartersnake (Thamnophis sirtalis tetrataenia) using demographic models.

For endangered species persisting in a few populations, reintroductions to unoccupied habitat are a popular conservation action to increase viability in the long term. Identifying the reintroduction strategy that is most likely to result in viable founder and donor populations is essential to optimally use resources available for conservation. The San Francisco gartersnake (Thamnophis sirtalis tetrataenia) is an endangered sub-species that persists in a small number of populations in a highly urbanized region of California. Most of the extant populations of San Francisco gartersnakes have low adult abundance and effective population size, heightening the need for establishment of more populations for insurance against the risk of extinction. We used simulations from demographic models to project the probability of quasi-extinction for reintroduced populations of San Francisco gartersnakes based on the release of neonate, juvenile, adult, or mixed-age propagules. Our simulation results indicated that the release of head-started juveniles resulted in the greatest viability of reintroduced populations, and that releases would need to continue for at least 15 years to ensure a low probability of quasi-extinction. Releasing captive-bred juvenile snakes would also have less effect on the viability of the donor population, compared to strategies that require more adult snakes to be removed from the donor population for translocation. Our models focus on snake demography, but the genetic makeup of donor, captive, and reintroduced populations will also be a major concern for any proposed reintroduction plan. This study demonstrates how modeling can be used to inform reintroduction strategies for highly imperiled species.

Advances in wildlife abundance estimation using pedigree reconstruction.

The conservation and management of wildlife populations, particularly for threatened and endangered species are greatly aided with abundance, growth rate, and density measures. Traditional methods of estimating abundance and related metrics represent trade-offs in effort and precision of estimates. Pedigree reconstruction is an emerging, attractive alternate approach because its use of one-time, noninvasive sampling of individuals to infer the existence of unsampled individuals. However, advances in pedigree reconstruction could improve its utility, including forming a measure of precision for the method, establishing required spatial sampling effort for accurate estimates, ascertaining the spatial extent of abundance estimates derived from pedigree reconstruction, and assessing how population density affects the estimator's performance. Using established relationships for a stochastic, spatially explicit simulated moose (Alces americanus) population, pedigree reconstruction provided accurate estimates of the adult moose population size and trend. Novel bootstrapped confidence intervals performed as expected with intensive sampling but underperformed with moderate sampling efforts that could produce abundance estimates with low bias. Adult population estimates more closely reflected the total number of adults in the extant population, rather than number of adults inhabiting the area where sampling occurred. Increasing sampling effort, measured as the proportion of individuals sampled and as the proportion of a hypothetical study area, yielded similar asymptotic patterns over time. Simulations indicated a positive relationship between animal density and sampling effort required for unbiased estimates. These results indicate that pedigree reconstruction can produce accurate abundance estimates and may be particularly valuable for surveying smaller areas and low-density populations.

Beyond protected areas: The importance of mixed-use landscapes for the conservation of Sumatran elephants (Elephas maximus sumatranus).

Elephants were once widely distributed across the Indonesian island of Sumatra but now exist in small, isolated populations. Using the best data available on elephant occurrence, we aimed to (a) predict potential habitat suitability for elephants (Elephas maximus sumatranus) across the island of Sumatra and (b) model landscape connectivity among the extant elephant populations. We used direct sightings and indirect observations of elephant signs, as well as six remotely sensed proxies of surface ruggedness, vegetation productivity and structure, and human land use and disturbance, to model habitat suitability in a Google Earth Engine (GEE) environment. We validated the habitat suitability prediction using 10-fold spatial block cross validation and by calculating the area under the precision-recall curve (AUC-PR), sensitivity, and specificity for each model iteration. We also used a geolocation dataset collected from global positioning system (GPS) collars fitted on elephants as an independent validation dataset. Models showed good predictive performance with a mean AUC-PR of 0.73, sensitivity of 0.76, and specificity of 0.68. Greater than 83% of the independent GPS collar geolocations were located in predicted suitable habitat. We found human modification, surface ruggedness, and normalized difference vegetation index to be the most important variables for predicting suitable elephant habitat. Thirty-two percent, or 135,646 km2, of Sumatra's land area was predicted to be suitable habitat, with 43 patches of suitable habitat located across Sumatra. Areas with high connectivity were concentrated in the Riau and North Sumatra provinces. Though our analysis highlights the need to improve the quality of data collected on Sumatran elephants, more suitable habitat remains on Sumatra than is used by known populations. Targeted habitat conservation, especially of the suitable habitat in and around the Lamno, Balai Raja, Tesso Tenggara, Tesso Utara, Bukit Tigapuluh, Seblat, Padang Sugihan, and Bukit Barisan Selatan ranges, may improve the long-term viability of this critically endangered species.

Interactions among rainfall, fire, forbs and non-native grasses predict occupancy dynamics for the endangered Pacific pocket mouse (Perognathus longimembris pacificus) in a Mediterranean-type ecosystem

It is important to understand species-habitat relationships to implement effective adaptive management for rare species. However, it can be challenging to assess habitat associations and their relationships to abiotic stressors in dynamic habitats without the insights that can be gained from long-term monitoring. We report results from the first six years of extensive track tube monitoring of the largest two of three remaining extant populations of federally endangered Pacific pocket mouse (Perognathus longimembris pacificus) in a coastal Mediterranean-type ecosystem on Marine Corps Base, Camp Pendleton in southern California, USA. We used dynamic occupancy and structural equation modeling to assess potential drivers of population trends that included habitat, fire history, rainfall, disturbance, and the presence of other small mammals. We found that the variables that best predicted mouse occupancy were moderate to high forb and perennial herb cover (40–80%), and moderate to high open ground (20–70%) and low non-native grass cover (<20%), Non-native grass cover (>20%) was also a strong predictor of lower PPM colonization and increased extinction probabilities, with the extent of non-native grass cover being strongly influenced by annual rainfall and recency of fire. Our study adds to the growing literature on effects of invasive annual grasses on native species in Mediterranean-type ecosystems. We suggest that habitat management could be based upon promotion of open forb and perennial herb dominated habitats with reduction of non-native grasses by prescribed fire and other methods. These types of spatial and temporal monitoring programs can support land managers by creating a monitoring and management feedback loop. They can reveal landscape and environmental variables associated with species persistence, inform habitat management goals, and help managers to assess the success of management actions on populations of conservation concern.

Checklist and molecular phylogenetics reveal three taxonomic novelties in Habenaria (Orchidaceae, Orchidoideae) from Chapada dos Veadeiros, Goiás, Brazil

A comprehensive checklist of Habenaria from Chapada dos Veadeiros, State of Goiás, was performed alongside morphologic and molecular phylogenetic studies, revealing three new taxa endemic to this region. A total of 61 taxa (59 species and two varieties) of Habenaria are recorded for Chapada dos Veadeiros, representing a two-fold increase compared to previous lists and comprising one of the greatest diversities of the genus in Brazil. Of this total, four taxa are locally endemic. Habenaria cultellifolia, until recently known only from the type collection, was rediscovered in the region after 127 years without records and represents this species’ only known extant population. Three proposed new taxa of Habenaria (H. minuticalcar J.A.N. Bat. &amp;#38; Bianch. sp. nov., H. proiteana J.A.N. Bat., A.A. Vale &amp;#38; Bianch. sp. nov., and H. lavrensis var. xanthodactyla J.A.N. Bat. &amp;#38; Bianch. var. nov.) are corroborated by molecular phylogenetic analyses based on nuclear and plastid markers. They are described, illustrated, tentatively assessed as threatened, and compared to phylogenetically and morphologically related species. Since some areas of this mountain range have not yet been floristically sampled, additional taxonomic novelties and new records are still expected in the future.