Poor reproductive success of Gray Vireos in a declining California population

Since the 1940s, populations of Gray Vireos (Vireo vicinior) in California have collapsed, presumably because of parasitism by Brown‐headed Cowbirds (Molothrus ater). In 2012 and 2013, we studied the vireo's nesting ecology to assess factors affecting two of California's largest remaining populations in the chaparral of San Diego County. Nest success was extremely low, with a model‐averaged probability of nest survival of only 0.08 (N = 95). More nest failures were due to predation (83%) than to cowbird parasitism (13%). Video‐recording at 30 nests revealed that California Scrub‐Jays (Aphelocoma californica) were the most common nest predator (67%). Of eight variables tested, height of shrubs surrounding the nest had the strongest negative influence on nest survival, but was more strongly correlated with cowbird parasitism than with jay predation. Despite frequent renesting, seasonal productivity was well below the level required to sustain a population, especially in northern San Diego County where we found no Gray Vireos at six of seven sites where they had been present from 1997 to 2001 and where cowbird parasitism was more frequent. The vireo's continuing range collapse contrasts with recent climate‐change models predicting a range expansion, highlighting the importance of demographic studies. Low nest success is likely contributing to population declines in California, and the additive effect of cowbird parasitism suppresses productivity. Conservation of Gray Vireos in California will likely require development of alternative approaches to cowbird and scrub‐jay control appropriate to sites widely scattered in rugged chaparral.     

Spatially explicit and multi-sourced genetic information is critical for conservation of an endangered plant species,San Diego thornmint (<Emphasis Type="Italic">Acanthomintha ilicifolia</Emphasis>)

San Diego thornmint Acanthomintha ilicifolia (Gray) Gray (Lamiaceae) is a winter herb restricted to San Diego county in the United States and Baja California Norte in Mexico. Historic records document 80 occurrences of this species, with 55 extant occurrences in San Diego County currently known. We compared three measures of genetic variation to inform ongoing conservation efforts: putatively neutral genetic structure revealed from isozyme markers, apparent cytogenetic variation confirmed using flow cytometry, and potentially adaptive morphological variation quantified in a common-garden study. Together, these data indicated that this rare endemic is genetically complex, revealing significant differentiation of neutral and potentially adaptive genetic variation among populations, and possessing at least two cytotypes, sometimes even within the same population. While additional study is required to resolve the extent of potential local adaptation in this species, conservation plans should limit the movement of germplasm among occurrences and monitor populations in order to limit potential long-term impacts to population viability. Given that these findings challenge the canonical model of genetic structure in rare plants (low genetic variation and limited genetic structure), we recommend guidelines to apply genetic information to conservation strategies.     

Influence of physical processes on the design,functioning and evolution of restored tidal wetlands in California (USA)

The performance of two intertidal wetland mitigation projects constructed by the California Department of Transportation (Caltrans) in the Sweetwater Marsh National Wildlife Refuge (SMNWR) in San Diego Bay was evaluated over 5 years. Most of the Sweetwater wetland complex has been altered this century, including diking (with subsequent subsidence), filling, modification of the tidal regime, freshwater inflow and sediment fluxes. The mitigation project goals included a range of functional criteria intended to support two endangered bird species (light-footed clapper rail and California least tern) and one endangered plant (salt marsh bird's-beak). While the mitigation projects have achieved some of the performance criteria established in the regulatory permits (particularly, those related to fish), vegetation criteria for one of the bird species have not been met. The initial grading (in relation to local tidal datums) should support the target plant species, but growth has been less than required. Shortcomings of the habitat include elevated soil and groundwater salinity, low nutrient levels (especially nitrogen, which is readily leached from the coarse substrate), and eroding topography (where a single oversized and overly sinous channel and the lower-than-natural marshpalin result in high velocity surface water flow and erosion). The failure to achieve a large plain at low-marsh elevations highlights the importance of a more complete understanding of the relationship between the site physical processes (topography, hydrology, climate, geomorphology), substrate conditions, and biotic responses.     

Plant–arthropod interactions of an endangered California lupine

The reintroduction of endangered plant species is an essential conservation tool. Reintroductions can fail to create resilient, self‐sustaining populations due to a poor understanding of environmental factors that limit or promote plant success. Biotic factors, specifically plant–arthropod interactions, have been shown to affect the establishment of endangered plant populations. Lupinus nipomensis (Nipomo Mesa lupine) is a state of California (California Rare Plant Rank: 1B.1) and federally (65 FR 14888) endangered endemic plant with only one extant population located along the central California coast. How arthropods positively or negatively interact with L. nipomensis is not well known and more information could aid conservation efforts. We conducted arthropod surveys of the entire L. nipomensis extant population in spring 2017. Observed arthropods present on L. nipomensis included 17 families, with a majority of individuals belonging to Thripidae. We did not detect any obvious pollinators of L. nipomensis, providing support for previous studies suggesting this lupine is capable of self‐pollinating, and observed several arthropod genera that could potentially impact the reproductive success of L. nipomensis via incidental pollination or plant predation.     

Isolation and characterization of 23 polymorphic microsatellite loci for a West Indian iguana (Cyclura pinguis) from the British Virgin Islands

Twenty-three polymorphic microsatellite markers were identified and characterized for Cyclura pinguis, a critically endangered species of lizard (Sauria: Iguanidae) native to Anegada Island in the British Virgin Islands. We examined variation at these loci for 39 C. pinguis, finding up to five alleles per locus and an average expected heterozygosity of 0.55. Allele frequency estimates for these microsatellite loci will be used to characterize genetic diversity of captive and wild C. pinguis populations and to estimate relatedness among adult iguanas at the San Diego Zoo that form the nucleus of a captive breeding programme for this critically endangered species.     

Nests in the cities: adaptive and non-adaptive phenotypic plasticity and convergence in an urban bird

Phenotypic plasticity plays a critical role in adaptation to novel environments. Behavioural plasticity enables more rapid responses to unfamiliar conditions than evolution by natural selection. Urban ecosystems are one such novel environment in which behavioural plasticity has been documented. However, whether such plasticity is adaptive, and if plasticity is convergent among urban populations, is poorly understood. We studied the nesting biology of an ‘urban-adapter’ species, the dark-eyed junco (Junco hyemalis), to understand the role of plasticity in adapting to city life. We examined (i) whether novel nesting behaviours are adaptive, (ii) whether pairs modify nest characteristics in response to prior outcomes, and (iii) whether two urban populations exhibit similar nesting behaviour. We monitored 170 junco nests in urban Los Angeles and compared our results with prior research on 579 nests from urban San Diego. We found that nests placed in ecologically novel locations (off-ground and on artificial surfaces) increased fitness, and that pairs practiced informed re-nesting in site selection. The Los Angeles population more frequently nested off-ground than the San Diego population and exhibited a higher success rate. Our findings suggest that plasticity facilitates adaptation to urban environments, and that the drivers behind novel nesting behaviours are complex and multifaceted.     

Influence of physical processes on the design, functioning and evolution of restored tidal wetlands in California (USA)

The performance of two intertidal wetland mitigation projects constructed by the California Department of Transportation (Caltrans) in the Sweetwater Marsh National Wildlife Refuge (SMNWR) in San Diego Bay was evaluated over 5 years. Most of the Sweetwater wetland complex has been altered this century, including diking (with subsequent subsidence), filling, modification of the tidal regime, freshwater inflow and sediment fluxes. The mitigation project goals included a range of functional criteria intended to support two endangered bird species (light-footed clapper rail and California least tern) and one endangered plant (salt marsh bird's-beak). While the mitigation projects have achieved some of the performance criteria established in the regulatory permits (particularly, those related to fish), vegetation criteria for one of the bird species have not been met. The initial grading (in relation to local tidal datums) should support the target plant species, but growth has been less than required. Shortcomings of the habitat include elevated soil and groundwater salinity, low nutrient levels (especially nitrogen, which is readily leached from the coarse substrate), and eroding topography (where a single oversized and overly sinous channel and the lower-than-natural marshpalin result in high velocity surface water flow and erosion). The failure to achieve a large plain at low-marsh elevations highlights the importance of a more complete understanding of the relationship between the site physical processes (topography, hydrology, climate, geomorphology), substrate conditions, and biotic responses.Corresponding editor: R.E. Turner     

Population genetics and conservation implications for the endangered delta smelt in the San Francisco Bay-Delta

Over the last two decades, the collapse of the endangered delta smelt (Hypomesus transpacificus) in the San Francisco Bay-Delta has resulted in politically charged conservation decisions, including the rationing of valuable Delta water for use in California agriculture and urban centers. A fundamental question remaining in delta smelt conservation is whether current management strategies have been appropriately designed to protect the remaining genetic variation in delta smelt populations, rather than merely mitigating the decline of the species. We used 15 microsatellite markers to characterize genetic variation within and among sampling regions on geographic and temporal scales, to estimate changes in effective population size over time, to determine if a genetic bottleneck exists and to define conservation management units for this species. A genetic bottleneck was detected in each of the four sampling years, and a significant decline in effective population size was observed between sampling years 2003 and 2007. We also detected a weak geographic signal in any given sampling year that was unsupported by temporal consistency of this signal. We assessed two strategies for defining conservation units, and concluded that continuing to manage the species as a single, panmictic population throughout its range is the most feasible management strategy. The results of this study will inform conservation decisions and provide an effective means for genetically monitoring this imperiled species.     

Roadless areas and biodiversity: a case study in Alabama,USA

Roadless areas are important for biodiversity maintenance and nature conservation but remain politically controversial due to conflicting interests of conservation and development. In this study, we applied a recently developed index of roadless volume (RV) across 67 counties of Alabama, USA as a case study to examine the relationships between roadless areas and local species richness. Our results indicated that with the increase of RV across counties, both the number of total fish and exotic fish species increased, but the relationship was not significant for endemic fish species. The number of both herpetofaunal and plant species also increased with the increasing RV. For all included species, there was a significant positive correlation between species richness and RV values. The number of endangered species decreased with the increase of RV per-capita. Wildfire occurrences increased with the increase of RV. Preserving roadless areas is an important component of biodiversity conservation.     

Eliciting and integrating expert knowledge to assess the viability of the critically endangered golden sun‐moth Synemon plana

The critically endangered golden sun‐moth Synemon plana occurs in urban fringe areas of southeastern Australia that are currently experiencing rapid and extensive development. The urban fringe is a complex and uncertain environment in which to manage threatened species with the intersection of fragmented natural habitats, built environments and human populations generating novel, poorly understood interactions. In this context, management frameworks must incorporate ecological processes as well as social considerations. Here, we explore how biodiversity sensitive urban design might improve the fate of the golden sun‐moth, and threatened species generally, in urban fringe environments. We: (i) developed an expert‐informed Bayesian Belief Network model that synthesizes the current understanding of key determinants of golden sun‐moth population viability at sites experiencing urbanizing pressure; (ii) quantified the nature and strength of cause‐effect relationships between these factors using expert knowledge; and (iii) used the model to assess expectations of moth population viability in response to different combinations of management actions. We predict that adult survival, bare ground cover and cover of resource plants are the most important variables affecting the viability of golden sun‐moth populations. We also demonstrate the potential for biodiversity sensitive urban design as a complementary measure to conventional management for this species. Our findings highlight how expert knowledge may be a valuable component of conservation management, especially in addressing uncertainty around conservation decisions when empirical data are lacking, and how structured expert judgements become critical in supporting decisions that may help ameliorate extinction risks faced by threatened species in urban environments.     

Preliminary distributional analysis of US endangered bird species

A first exploration of applications of ecological niche modeling and geographic distributional prediction to endangered species protection is developed. Foci of richness of endangered bird species are identified in coastal California and along the southern fringe of the United States. Species included on the Endangered Species List on the basis of peripheral populations inflate these concentrations considerably. Species without protection in the US National Park System are focused particularly in peninsular Florida. Application of this methodology to additional taxa and regions holds promise for diverse conservation applications.     

Adaptive management assists reintroduction as higher tides threaten an endangered salt marsh plant

In theory, extirpated plant species can be reintroduced and managed to restore sustainable populations. However, few reintroduced plants are known to persist for more than a few years. Our adaptive‐management case study illustrates how we restored the endangered hemiparasitic annual plant, Chloropyron maritimum subsp. maritimum (salt marsh bird's beak), to Sweetwater Marsh, San Diego Bay National Wildlife Refuge, California, United States, and used monitoring and experimentation to identify the factors limiting the reintroduced population. After extirpation in 1988, reintroduction starting that year led to a resilient, genetically diverse population in 2016 (a “boom” of approximately 14,000) that rebounded from a “bust” (62 in 2014). Multiple regressions attributed 82% of the variation in population counts to tidal amplitude, rainfall, and temperature. Populations of salt marsh bird's beak crashed when the diurnal tide range peaked during the 18.6‐year lunar nodal cycle (a rarely considered factor that periodically added approximately 12 cm to tidal ranges). We explain booms as follows: During smaller tidal amplitudes, above‐average rainfall could desalinize upper intertidal soils and stimulate salt marsh bird's beak germination. Then, moderate temperature in May favors growth to reproduction in June. In addition, salt marsh bird's beak needs a short and open canopy of native perennial plants, with roots to parasitize (not non‐native annual grass pseudohosts) and nearby upland soil for a preferred pollinator, ground‐burrowing bees. Although our reintroduced salt marsh bird's beak population is an exceptional case of persistence, this rare species‐specific environmental and biological requirement makes it vulnerable to rising sea levels and global warming.     

The emergence of Cochlodinium along the California Coast (USA)

A sudden and nearly synchronous emergence of the red tide forming dinoflagellate Cochlodinium along more than 800 km of California coastline was initially observed in late summer 2004. Thereafter high cell concentrations have been detected on an annual basis. Here, we present quantitative and semi-quantitative data indicating that Cochlodinium was uncommon in the phytoplankton community in California prior to 2004 and is now persisting as a more regular component and one that seasonally can cause red tides. The quantitative portion of this study was primarily conducted in Monterey Bay, where cell densities reached at least 6 × 10⁴ cells L⁻¹ during the initial outbreak. A semi-quantitative comparison of California coastal counties by the California Department of Health Services (CDHS) was also made: of the 15 counties surveyed (most with multiple sites per county), cells were detected only from Los Angeles County in the south to San Mateo County in the central region (seven counties), but not in the northern part of the state (six counties). Two counties in the central region of the state, San Luis Obispo and Santa Cruz, displayed intense and frequent periods of elevated Cochlodinium cell abundances. Although not observed in the state-wide CDHS survey, we occasionally found cells in San Diego County with densities up to 2.7 × 10⁴ cells L⁻¹. Though these colonial dinoflagellates have been recognized in California for over 80 years, with several “blooms” recorded prior to 2004, the species’ geographic range and abundance in recent years suggest significant shifts in the nearshore phytoplankton community of this region of the eastern Pacific.     

Mortality from unintentional injuries in California, 1985.

In 1985 unintentional injuries were the fourth leading cause of death among California residents, causing 10,380 deaths. They were the leading cause of potential life lost, accounting for 278,109 years lost. This was more than twice the number of years lost due to heart disease and 1 1/2 times the number lost due to cancer. Motor vehicle traffic accidents were the leading cause of unintentional injury deaths, accounting for half (5,158) the deaths. The next two leading causes were poisoning (especially for men aged 25 to 44 years) and falls (especially among persons aged 75 and older). Drowning was second to motor vehicle accidents as a cause of death in children aged 1 to 14 years. California''s age-adjusted injury mortality rates in 1985 were lower in coastal and urban counties than in inland and rural counties, and these rates were generally lower in counties having organized systems of trauma care.     

Genetic differences between the endangered San Clemente Island loggerhead shrike Lanius ludovicianus mearnsi and two neighbouring subspecies demonstrated by mtDNA control region and cytochrome b sequence variation

We investigated mtDNA sequence variation in five populations of the loggerhead shrike Lanius ludovicianus , representing four subspecies, including the San Clemente loggerhead shrike L. l. mearnsi , a critically endangered California Channel Island endemic. Variability in 200 bp of control region and 200 bp of cytochrome b was extremely low, and defined four haplotypes. Strong structure was apparent among all three southern Californian subspecies, including L. l. mearnsi , with one haplotype predominating in each subspecies. Although potential levels of gene flow between L. l. mearnsi and neighbouring populations are low, mtDNA data support field observations that some shrikes visit the island during winter but do not stay to breed, and suggest that these birds come from the mainland. The similarity in haplotypes between populations from Saskatchewan, Canada and those in southern California suggests post-glacial northern range expansion of the species. Our results confirm the evolutionary distinctiveness of L. l. mearnsi and justify continuing efforts for its conservation.     

Landscape genetics of an endangered salt marsh endemic: Identifying population continuity and barriers to dispersal

Preserving the genetic diversity of endangered species is fundamental to their conservation and requires an understanding of genetic structure. In turn, identification of landscape features that impede gene flow can facilitate management to mitigate such obstacles and help with identifying isolated populations. We conducted a landscape genetic study of the endangered salt marsh harvest mouse (Reithrodontomys raviventris), a species endemic to the coastal marshes of the San Francisco Estuary of California. We collected and genotyped?>?500 samples from across the marshes of Suisun Bay which contain the largest remaining tracts of habitat for the species. Cluster analyses and a population tree identified three geographically discrete populations. Next, we conducted landscape genetic analyses at two scales (the entire study area and across the Northern Marshes) where we tested 65 univariate models of landscape features and used the best supported to test multivariable analyses. Our analysis of the entire study area indicated that open water and elevation (>?2 m) constrained gene flow. Analysis of the Northern Marshes, where low elevation marsh habitat is more continuous, indicated that geographic distance was the only significant predictor of genetic distance at this scale. The identification of a large, connected population across Northern Marshes achieves a number of recovery targets for this stronghold of the species. The identification of landscape features that act as barriers to dispersal enables the identification of isolated and vulnerable populations more broadly across the species range, thus aiding conservation prioritization.

     

Effects of introduced species on floristic similarity: Comparing two US states

This study aims to examine the effects of introduced species on increasing (homogenizing) or decreasing (differentiating) floristic similarity of plant composition. We calculated the Jaccard index for each pair of counties within two states of USA, California and Florida. We computed the Jaccard index separately for all (native plus exotic) species, for native species, and for exotic species. We further calculated a homogenization index between all species and native species for each pair of counties by subtracting similarity index for native species from that for all species. We correlated the Jaccard and homogenization indices to geographic distance, latitude separation, and longitude separation between pairs of counties and to average human population density and average land area of the two counties. We find a very strong pattern of differentiation for introduced species among nearly all Florida counties. In California, introduced species have a differentiating effect in about half the comparisons. We also find that introduced species tend to have a more homogenizing (or less differentiating) effect with increasing distances between counties. Our results do not show a clear relationship between human population density and the homogenization index.     

Range and Frequency of Africanized Honey Bees in California (USA)

Africanized honey bees entered California in 1994 but few accounts of their northward expansion or their frequency relative to European honey bees have been published. We used mitochondrial markers and morphometric analyses to determine the prevalence of Africanized honeybees in San Diego County and their current northward progress in California west of the Sierra Nevada crest. The northernmost African mitotypes detected were approximately 40 km south of Sacramento in California’s central valley. In San Diego County, 65% of foraging honey bee workers carry African mitochondria and the estimated percentage of Africanized workers using morphological measurements is similar (61%). There was no correlation between mitotype and morphology in San Diego County suggesting Africanized bees result from bidirectional hybridization. Seventy percent of feral hives, but only 13% of managed hives, sampled in San Diego County carried the African mitotype indicating that a large fraction of foraging workers in both urban and rural San Diego County are feral. We also found a single nucleotide polymorphism at the DNA barcode locus COI that distinguishes European and African mitotypes. The utility of this marker was confirmed using 401 georeferenced honey bee sequences from the worldwide Barcode of Life Database. Future censuses can determine whether the current range of the Africanized form is stable, patterns of introgression at nuclear loci, and the environmental factors that may limit the northern range of the Africanized honey bee.     

Interspecies mating in sympatric species of Syngnathus pipefish

Hybridization is thought to be an important source of novel genetic variation, and interspecific hybridization may increase the adaptive potential of wild populations. While hybridization has not been previously reported in syngnathid fishes (seahorses and pipefish), the sympatric occurrence of closely related species at high densities increases the probability of interspecies mating in this group. Southern California is home to five species of Syngnathus pipefish, and these species frequently co-occur in near-shore eelgrass beds along the California coast. Recent work has identified exceptionally high levels of genetic diversity in southern populations of Syngnathus leptorhynchus, a widespread species which ranges from Mexico to Alaska. Microsatellite genotyping and mitochondrial sequence data are used here to study the population genetics of S. leptorhynchus and S. auliscus at a site in San Diego Bay where they are found to co-occur at high densities. While no adult hybrids were detected in the study population, analysis of male broods indicates that interspecies mating is occurring between the two species. The lack of premating isolating mechanisms between these two relatives suggests that hybridization may be common in sympatric species of Syngnathus.     

Using species distribution modeling to set management priorities for mammals in northern Thailand

Rapid deforestation has occurred in northern Thailand and is expected to continue. Thus, identification and protection of sufficient amounts of the highest quality habitat is urgent. Wildlife occurrence data were gathered along wildlife trails and patrolling routes in protected areas and forest patches outside of protected areas. Geographic Information Systems, bio-physical and anthropogenic variables were used to generate suitable habitats for 17 mammal species using maximum entropy theory (MAXENT). Suitable habitats for all species were aggregated, and used to set priorities for wildlife conservation in northern Thailand. In addition, predicted deforestation was overlaid on moderate and high priority areas to determine future wildlife threats and aid decision-making concerning which areas to protect. The results revealed that the total extent of suitable habitats for the studied species covers approximately 37% of the region. Nearly 70% of the total habitat for endangered and vulnerable species is predicted in large and contiguous protected areas. Threatened areas with high biodiversity encompass approximately 1.9% of the region, and 66% of this figure is predicted to occur in existing protected areas. Based on the model outcomes, we recommend reducing human pressures, enhancing the density of prey species and conservation outside protected areas, as well as increasing connectivity of suitable habitats among protected areas that are too small to maintain viable populations in isolation.