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At least 19 recordsLinked to original sources

A comment on "bats killed in large numbers at United States wind energy facilities"

Widespread reports of bat fatalities caused by wind turbines have raised concerns about the impacts of wind power development. Reliable estimates of the total number killed and the potential effects on populations are needed, but it is crucial that they be based on sound data. In a recent BioScience article, Hayes (2013) estimated that over 600,000 bats were killed at wind turbines in the United States in 2012. The scientific errors in the analysis are numerous, with the two most serious being that the included sites constituted a convenience sample, not a representative sample, and that the individual site estimates are derived from such different methodologies that they are inherently not comparable. This estimate is almost certainly inaccurate, but whether the actual number is much smaller, much larger, or about the same is uncertain. An accurate estimate of total bat fatality is not currently possible, given the shortcomings of the available data.

BioScience↗

An incomplete analysis

Niles and colleagues (2009) do not present all of the data relevant to the issues they address in the article they wrote for BioScience. They reference unnamed sources for pre-1997 horseshoe crab harvest to conclude that recent harvest exceeds historic harvest. In fact, reported landings from New Jersey, Delaware, Maryland, and Virginia in 2006 (352 metric tons [mt]) were between landings in 1989 (365 mt) and 1990 (232 mt) (www.st.nmfs.noaa.gov/st1/commercial/inaex.html), despite nonmandatory reporting coastwide before 1998 (Kreamer and Michels 2009). They present egg densities from New Jersey beaches only. Of the 11 Delaware beaches sampled, eggs in the top 5 centimeters exceeded their monitoring target of 50,000 per square meter at 5 in 2006 and at 6 in 2007 (Kalasz et al. 2008). They rely on the Delaware trawl survey for historic trends. Nine fishery-independent surveys have been used to assess trends in the Delaware Bay region, and several began before 1990 (Smith et al. 2009a).

BioScience↗

Wolves will not provide small-scale ecological restoration

Licht and colleagues (BioScience 60: 147–153) proposed a paradigm shift in wolf management to include the introductions of small, highly manipulated groups of wolves ( Canis lupus ) to confined natural areas to facilitate ecosystem recovery. Certainly, reductions or losses of apex predators from many regions worldwide have had profound effects on ecosystem characteristics (Soulé et al. 2003). Numerous efforts to restore or enhance predator populations through policy change or reintroductions have occurred, often with the intent to restore ecosystem function (Breitenmoser et al. 2001). However, in addition to the gargantuan technological and political challenges inherent in Licht and colleagues' proposal, we contend that intensively managed wolves will not restore natural ecosystem processes given the disparity in scale between these proposed actions and the ecosystem processes that wolves foster. Further, we note that predator-prey relationships are more complex than Licht suggested.

BioScience↗

The Global Invasive Species Information Network: What's in it for you?

A well-known article in BioScience — probably the most widely cited scientific study on invasive species in recent years—calculated the annual cost of invasive species in the United States alone at $138 billion per year (Pimentel et al. 2000). The total annual cost of invasive species to human societies worldwide can therefore be estimated to be in the hundreds of billions of dollars, including the costs of control, detrimental effects on human health, and losses in agricultural production and ecosystem services. This enormous sum far exceeds the combined annual cost of all natural disasters (Munich Re Group 2004), making the problem of invasive species in both agricultural and natural ecosystems a high-priority issue. But there is hope for counteracting the invasive species challenge, and much of that hope stems from new strategies being developed for managing information about invasive species and their effects.

BioScience↗

Alternative interpretations of oil spill data

In his article "Oil, Seabirds, and Science" (BioScience 46: 587-597), John Wiens attempted to review Exxon Valdez oil spill (EVOS) damage assessment studies and the politics of EVOS science in one stroke. In my opinion, neither purpose was particularly well served.

Alaska↗

Restricting wolves risks escape

Implementing the proposal set forth by Licht and colleagues ( BioScience 60: 147–153) requires restricting wolves to tiny "islands," areas that are magnitudes smaller than the ranges of most wolf populations. Wolves naturally have large ranges; restricting their spatial needs increases the risk of wolves escaping, exacerbating public relations and political and legal problems. These problems would not be solved by (a) scaring back straying radioed wolves; (b) controlling reproduction; or (c) the use of physical, virtual, or biological barriers. The problem is not wolves breeding; it is wolves killing livestock and pets, or at least people fearing they will. Standard wolf-proof barriers are 10-feet-high, chain-link fences with a 4-foot apron buried 2-feet below ground. Virtual fences, shock-collars with electrodes continually touching the skin, and frequent battery replacement are all problematic, even for captive wolves (Shivik et al. 2002). Scent-marking and howling, controls suggested by Licht and colleagues, can affect wolf movements, but our research demonstrates that trespass is common (Mech 1994). The prospects for public tolerance of such costly and intensive management seems dim anytime soon.

BioScience↗

Reference genome of the California glossy snake, Arizona elegans occidentalis: A declining California Species of Special Concern

The glossy snake ( Arizona elegans ) is a polytypic species broadly distributed across southwestern North America. The species occupies habitats ranging from California’s coastal chaparral to the shortgrass prairies of Texas and southeastern Nebraska, to the extensive arid scrublands of central México. Three subspecies are currently recognized in California, one of which is afforded state-level protection based on the extensive loss and modification of its preferred alluvial coastal scrub and inland desert habitat. We report the first genome assembly of A. elegans occidentalis as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technologies to produce a de novo assembled genome. The assembly comprises a total of 140 scaffolds spanning 1,842,602,218 base pairs, has a contig NG50 of 61 Mb, a scaffold NG50 of 136 Mb, and a BUSCO complete score of 95.9%, and is one of the most complete snake genome assemblies. The A. e. occidentalis genome will be a key tool for understanding the genomic diversity and the basis of adaptations within this species and close relatives within the hyperdiverse snake family Colubridae.

California↗

Reference genome of an iconic lizard in western North America, Blainville’s horned lizard Phrynosoma blainvillii

Genome assemblies are increasingly being used to identify adaptive genetic variation that can help prioritize the population management of protected species. This approach may be particularly relevant to species like Blainville’s horned lizard, Phrynosoma blainvillii , due to its specialized diet on noxious harvester ants, numerous adaptative traits for avoiding predation (e.g. cranial horns, dorsoventrally compressed body, cryptic coloration, and blood squirting from the orbital sinuses), and status as Species of Special Concern in California. Rangewide decline since the early 20th century, the basis of its conservation status, has been driven mainly by habitat conversion, over-collecting, and invasion of a non-native ant that displaces its native ant prey base. Here, we report on a scaffold-level genome assembly for P. blainvillii as part of the California Conservation Genomics Project (CCGP), produced using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology. The de novo assembly has 78 scaffolds, a total length of ~2.21 Gb, a scaffold N50 length of ~352 Mb, and BUSCO score of 97.4%. This is the second species of Phrynosoma for which a reference genome has been assembled and represents a considerable improvement in terms of contiguity and completeness. Combined with the landscape genomics data being compiled by the CCGP, this assembly will help strategize efforts to maintain and/or restore local genetic diversity, where interventions like genetic rescue, translocation, and strategic land preservation may be the only means by which P. blainvillii and other low-vagility species can survive in the fragmented habitats of California.

California↗

Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis

Spiny lizards (genus Sceloporus ) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis , is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland to chaparral to open woodlands. As small ectotherms, Sceloporus lizards are particularly vulnerable to climate change, and S. occidentalis has also become an important system for studying the impacts of land use change and urbanization on small vertebrates. Here, we report a new reference genome assembly for S. occidentalis , as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomics strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 608 scaffolds spanning 2,856 Mb, has a contig N50 of 18.9 Mb, a scaffold N50 of 98.4 Mb, and BUSCO completeness score of 98.1% based on the tetrapod gene set. This reference genome will be valuable for understanding ecological and evolutionary dynamics in S. occidentalis , the species status of the California endemic island fence lizard ( S. becki ), and the spectacular radiation of Sceloporus lizards.

California↗

A genome assembly for the southern Pacific rattlesnake, Crotalus oreganus helleri, in the western rattlesnake species complex

Rattlesnakes play important roles in their ecosystems by regulating prey populations, are involved in complex coevolutionary dynamics with their prey, and exhibit a variety of unusual adaptations, including maternal care, heat-sensing pit organs, hinged fangs, and medically-significant venoms. The western rattlesnake ( Crotalus oreganus ) is one of the widest ranging rattlesnake species, with a distribution from British Columbia, where it is listed as threatened, to Baja California and east across the Great Basin to western Wyoming, Colorado and New Mexico. Here, we report a new reference genome assembly for one of six currently recognized subspecies, C. oreganus helleri , as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomic sequencing strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 698 scaffolds spanning 1,564,812,557 base pairs, has a contig N50 of 64.7 Mb, a scaffold N50 of 110.8 Mb, and BUSCO complete score of 90.5%. This reference genome will be valuable for studies on the genomic basis of venom evolution and variation within Crotalus , in resolving the taxonomy of C. oreganus and its relatives, and for the conservation and management of rattlesnakes in general.

California↗

A chromosome-level genome assembly of a vernal pool specialist amphibian, the Western Spadefoot, Spea hammondii

We assembled and annotated a chromosome-level genome for the Western Spadefoot, Spea hammondii (Anura, Scaphiopodidae) representing one of only three amphibians included in the California Conservation Genomics Project (CCGP). Spea hammondii is a vernal pool breeding anuran native to California and northwestern Baja California which has undergone both range contractions and local extirpations across its distribution, primarily due to habitat loss and degradation and drought. The species is recognized by the state of California as a Species of Special Concern and is proposed for listing under the United States Endangered Species Act. Using the established CCGP pipeline, this S. hammondii genome was produced using Pacific Biosciences HiFi long-reads and Omni-C proximity ligation, resulting in a de novo genome assembly 1.14 Gb in length, distributed across 479 scaffolds (scaffold N50 = 120.8 Mb; largest scaffold = 183.6 Mb) with a BUSCO completeness score of 90.9% using a conserved tetrapod ortholog set. Our assembly shows high base accuracy (quality value [QV] = 63.7) and low frameshift error in coding regions (QV 50.42). Annotation of this genome yielded 20,434 genes with a BUSCO completeness score of 94.7%. This genome assembly, in combination with range-wide resequencing data from CCGP, will facilitate statewide population genomic assessments to delineate conservation units, quantify inbreeding and genomic load, and test for adaptive variation associated with vernal pool hydrology and drought tolerance, all of which are important considerations in the proposed federal listing.

Journal of Heredity↗

A chromosome-level genome assembly of a vernal pool specialist amphibian, the Western Spadefoot, Spea hammondii

We assembled and annotated a chromosome-level reference genome for the Western Spadefoot, Spea hammondii (Anura, Scaphiopodidae) representing one of only three amphibians included in the California Conservation Genomics Project (CCGP). Spea hammondii is a vernal pool breeding anuran native to California and northwestern Baja California which has undergone both range contractions and local extirpations across its distribution, primarily due to habitat loss and degradation and drought. The species is recognized by the state of California as a Species of Special Concern and is proposed for listing under the United States Endangered Species Act. Using the established CCGP pipeline, this S. hammondii genome was produced using Pacific Biosciences HiFi long-reads and Omni-C proximity ligation, resulting in a de novo genome assembly 1.14 Gb in length, distributed across 479 scaffolds (scaffold N50 = 120.8 Mb; largest scaffold = 183.6 Mb) with a BUSCO completeness score of 90.9% using a conserved tetrapod ortholog set. Our assembly shows high base accuracy (QV = 63.7) and low frameshift error in coding regions (QV 50.42). Annotation of this genome yielded 20,434 genes with a BUSCO completeness score of 94.7%. This reference genome, in combination with range-wide resequencing data from CCGP, will facilitate statewide population genomic assessments to delineate conservation units, quantify inbreeding and genomic load, and test for adaptive variation associated with vernal pool hydrology and drought tolerance, all of which are important considerations in the proposed federal listing.

BioRxiv↗

Sea-level rise and coastal forests on the Gulf of Mexico

In this report, we review literature pertaining to the response of coastal forests on the Gulf of Mexico to sea-level rise. The report is divided into chapters that discuss effects of sea-level rise on non-mangrove forests, effects of sea-level rise on mangrove forests, and responses of Gulf coast trees to increased flooding and salinity. An assessment of the extent of coastal forest likely to be affected by sea-level rise in the near future is beyond the scope of this report. Chapter 1 discusses sea-level effects on non-mangrove forests of the Gulf of Mexico including descriptions of how coastlines and, therefore, coastal forests have changed through the Holo~ene, a discussion of how coastal geomorphology and hydrology may affect interactions of coastal forest with sea-level rise, and an evaluation of the role that hurricanes might play in coastal forest retreat. Literature on geological changes throughout the Holocene is not fully reviewed; sufficient information is given to place current rates of coastal forest retreat into historical perspective. Similarly, effects of hurricanes on coastal forests are not fully reviewed. Information that is pertinent to the role of hurricanes in coastal forest retreat and to the effects of hurricanes on the forest's interaction with sea level is presented. For more extensive reviews of hurricane effects on coastal forests of the Caribbean and the southeastern United States, the reader is referred to issues of BioScience (1994, Vol 44, no. 4), Biotropica (1991, "Special Issue: Ecosystem, Plant, and Animal Responses to Hurricanes in the Caribbean", Vol. 23, No. 4, Part A) and the Journal of Coastal Research (1991, "Impacts of Hurricane Hugo, Special Issue No. 8; and 1995, "Imprcts of Hurricane Andrew on the Coastal Zones of Florida and Louisiana: 22-26 August 1992", Special Issue No. 21). Selected pertinent information from Virginia, South and North Carolina has been included in this review, because much of our knowledge of coastal forest response to hurricanes, salinity and flooding comes from the Atlantic coast. These areas are floristically similar to the northern Gulf of Mexico. Species distribution of coastal forest trees and shrubs on the Gulf of Mexico are listed in Appendix 1. Extensive research has been conducted on the responses of individual tree species to increased salinity and flooding. Synthesis of this research, although very important for evaluating effects of sea-level rise and various hydrological modifications on coastal forest, is beyond the scope of this review. These studies are included as an annotated bibliography (Appendix 2). Selected field studies on tree responses to changes in hydrology and salinity (impoundments, drainage, etc.) are referenced in Appendix 3. A review of mangrove response to sea-level rise is included in Chapter 2. Mangrove forests are discussed in the context of Holocene changes in geomorphology. Predictions of the fate of mangroves in the face of future sea-level rise, as well as a review of factors that affect interactions between mangroves and sea-level rise are discussed. Selected references from outside the United States are included, because much of our knowledge of how mangroves react to sea-level rise comes from other tropical areas of the world. A discussion of hurricane effects on the mangroves of south Florida highlights gaps in our knowledge of how hurricanes affect responses of mangrove vegetation to sea-level rise there. Mangrove responses to temperature and elevated CO2 are briefly mentioned. These factors, as well as sea level, are expected to change in the future and may affect mangrove distribution.

Open-File Report↗

Lithobates sylvaticus (wood frog). Habitat use.

Lithobates sylvaticus is the second most widely distributed anuran in North America (Martof and Humphries 1959. Am. Midl. Nat. 61:350–389), and its habitat use reflects the environmental variation that exists across its geographic range (Semlitsch et al. 2009. BioScience 59:853–862). Although L. sylvaticus post-breeding habitat selection has been described in Missouri (Rittenhouse and Semlitsch 2007. J. Herpetol. 41:645–653) and Maine (Baldwin et al. 2006. J. Herpetol. 40:442–453; Blomquist and Hunter 2010. Ecoscience 17:251–264), these studies did not report the species’ use of glacial erratics, or boulders. We conducted our study in Maine’s Nahmakanta Public Reserved Land (45.68210°N, 69.12940°W, WGS84; 407–530 m elev.), which is located in the Quebec/New England Boundary Mountains ecoregion.

Maine↗

Bet-hedging applications for conservation

One of the early tenets of conservation biology is that population viability is enhanced by maintaining multiple populations of a species. The strength of this tenet is justified by principles of bet-hedging. Management strategies that reduce variance in population size will also reduce risk of extinction. Asynchrony in population fluctuations in independent populations reduces variance in the aggregate of populations whereas environmental correlation among areas increases the risk that all populations will go extinct. We review the theoretical rationale of bet-hedging and suggest applications for conservation management of least terns in Nebraska and grizzly bears in the northern Rocky Mountains of the United States. The risk of extinction for least terns will be reduced if we can sustain the small central Platte River population in addition to the larger population on the lower Platte. Similarly, by restoring grizzly bears to the Bitterroot wilderness of Idaho and Montana can reduce the probability of extinction for grizzly bears in the Rocky Mountains of the United States by as much as 69-93%.

Journal of Biosciences↗

Dynamics of a plant-herbivore-predator system with plant-toxicity

A system of ordinary differential equations is considered that models the interactions of two plant species populations, an herbivore population, and a predator population. We use a toxin-determined functional response to describe the interactions between plant species and herbivores and use a Holling Type II functional response to model the interactions between herbivores and predators. In order to study how the predators impact the succession of vegetation, we derive invasion conditions under which a plant species can invade into an environment in which another plant species is co-existing with a herbivore population with or without a predator population. These conditions provide threshold quantities for several parameters that may play a key role in the dynamics of the system. Numerical simulations are conducted to reinforce the analytical results. This model can be applied to a boreal ecosystem trophic chain to examine the possible cascading effects of predator-control actions when plant species differ in their levels of toxic defense.

Mathematical Biosciences↗

Effects of dispersal on total biomass in a patchy, heterogeneous system: Analysis and experiment

An intriguing recent result from mathematics is that a population diffusing at an intermediate rate in an environment in which resources vary spatially will reach a higher total equilibrium biomass than the population in an environment in which the same total resources are distributed homogeneously. We extended the current mathematical theory to apply to logistic growth and also showed that the result applies to patchy systems with dispersal among patches, both for continuous and discrete time. This allowed us to make specific predictions, through simulations, concerning the biomass dynamics, which were verified by a laboratory experiment. The experiment was a study of biomass growth of duckweed ( Lemna minor Linn.), where the resources (nutrients added to water) were distributed homogeneously among a discrete series of water-filled containers in one treatment, and distributed heterogeneously in another treatment. The experimental results showed that total biomass peaked at an intermediate, relatively low, diffusion rate, higher than the total carrying capacity of the system and agreeing with the simulation model. The implications of the experiment to dynamics of source, sink, and pseudo-sink dynamics are discussed.

Mathematical Biosciences↗

Book review: Quasispecies as a unifying concept in population dynamics

The quasispecies concept had two independent origins. One source was the theoretical ideas of Manfred Eigen and Peter Schuster in the 1970s. Studying the self-organization and evolution of primitive RNA molecules, they defined quasispecies as a distribution of mutant viral genomes generated by the mutation-selection process. In particular, the quasispecies nucleotide distribution consists of a singular fittest genotype, called the master sequence, surrounded by similar mutant spectra. The other source of the quasispecies concept can be traced to the growing empirical knowledge on RNA viruses formulated around the same time. Genomic sequencing of viral RNA indicated a variety of nucleotide sequences, or a distribution of sequences. Mutations in both Eigen’s theoretical system in the RNA viruses are not rare, as RNA is structurally less stable than RNA, but common, preventing the fittest genotype from becoming dominant. Virologists have adopted the quasispecies concept, with some papers on Covid-19 using the construct to explain that virus’s behavior.

Mathematical Biosciences↗