Tripartite genetic subdivisions in the ornate shrew (Sorex ornatus)

We examined cytochrome b sequence variation in 251 ornate shrews (Sorex ornatus) from 20 localities distributed throughout their geographical range. Additionally, vagrant (S. vagrans) and montane (S. monticolus) shrews from four localities were used as outgroups. We found 24 haplotypes in ornate shrews from California (USA) and Baja California (Mexico) that differed by 1-31 substitutions in 392 bp of mitochondrial DNA (mtDNA) sequence. In a subset of individuals, we sequenced 699 bp of cytochrome b to better resolve the phylogeographic relationships of populations. The ornate shrew is phylogeographically structured into three haplotype clades representing southern, central and northern localities. Analysis of allozyme variation reveals a similar pattern of variation. Several other small California vertebrates have a similar tripartite pattern of genetic subdivision. We suggest that topographic barriers and expansion and contraction of wetland habitats in the central valley during Pleistocene glacial cycles account for these patterns of genetic variation. Remarkably, the northern ornate shrew clade is phylogenetically clustered with another species of shrew suggesting that it may be a unique lowland form of the vagrant shrew that evolved in parallel to their southern California counterparts.     

Characterization of seven polymorphic microsatellite loci in the Baja California endemic black‐tailed brush lizard Urosaurus nigricaudus

Seven microsatellite loci were developed for the Baja California endemic black‐tailed brush lizard Urosaurus nigricaudus, using an enriched genomic DNA library. All loci were polymorphic and overall presented high levels of variation. Number of alleles ranged from five to 16 (average 12.14), and observed heterozygosities from 0.535 to 0.923 (average 0.752). Cross‐species amplification was successful and polymorphism was detected for all the loci using the congeners Urosaurus lahtelai and Urosaurus ornatus. These markers will be useful to study fragmented populations of U. nigricaudus on agricultural landscape of the Baja California Peninsula.     

Factors influencing the variation in capture rates of shrews in southern California,USA

We examined the temporal variation in capture rates of shrewsNotiosorex crawfordi (Coues, 1877) and Sorex ornatus (Merriam, 1895) in 20 sites representing fragmented and continuous habitats in southern California, USA. InN. crawfordi, the temporal variation was significantly correlated with the mean capture rates. Of the 6 landscape variables analyzed (size of the landscape, size of the sample area, altitude, edge, longitude and latitude), sample area was positively correlated with variation in capture rates ofN. crawfordi. InS. ornatus, longitude was negatively correlated with variation in capture rates. Analysis of the effect of precipitation on the short- and long-term capture rates at 2 of the sites showed no correlation between rainfall and capture rates of shrews even though peak number of shrews at both sites were reached during the year of highest amount of rainfall. A key problem confounding capture rates of shrews in southern California is the low overall abundance of both shrew species in all habitats and seasons.     

Population genetic structure of Sorex unguiculatus and Sorex caecutiens (Soricidae, Mammalia) in Hokkaido, based on microsatellite DNA polymorphism

We investigated the genetic structure of Sorex unguiculatus and Sorex caecutiens populations in Hokkaido, Japan, using hypervariable microsatellite DNA markers. We used five microsatellite loci to type 475 S. unguiculatus individuals from 20 localities on the Hokkaido mainland and four localities from each of four offshore islands (and 11 shrews from one locality in southern Sakhalin for a particular analysis). We used six microsatellite loci to type 240 S. caecutiens individuals from 13 localities on the Hokkaido mainland. Genetic variation was high in mainland populations of both species and low in the island populations of S. unguiculatus. Allelic richness and island size were positively correlated for S. unguiculatus, suggesting that genetic drift occurred on those islands due to small population size. In addition, four insular populations of S. unguiculatus were genetically differentiated from the mainland populations, although clear phylogeographic clustering was not confirmed among populations on the Hokkaido mainland for either S. unguiculatus or S. caecutiens. Heterozygosity excess was observed in more than half of the populations including the mainland populations of the two species, suggesting recent bottleneck events in these populations. Population dynamics of the shrews might be explained by a metapopulation scheme. According to autocorrelation analysis, the extent of non-random spatial genetic structure was approximately 100 km. Isolation by distance was observed in S. unguiculatus, but not in S. caecutiens although there is a positive trend. The lack of correlation for S. caecutiens might have been due to small sample size. Thus, no obvious differences in population genetic structure were found between the two species on the Hokkaido mainland in the present study, while previous investigations using mitochondrial DNA sequences inferred that these two species might have rather different biogeographic histories.     

Oceanographic Currents and Local Ecological Knowledge Indicate,and Genetics Does Not Refute,a Contemporary Pattern of Larval Dispersal for The Ornate Spiny Lobster,Panulirus ornatus in the South-East Asian Archipelago

Here we utilize a combination of genetic data, oceanographic data, and local ecological knowledge to assess connectivity patterns of the ornate spiny lobster Panulirus ornatus (Fabricius, 1798) in the South-East Asian archipelago from Vietnam to Australia. Partial mitochondrial DNA control region and 10 polymorphic microsatellites did not detect genetic structure of 216 wild P. ornatus samples from Australia, Indonesia and Vietnam. Analyses show no evidence for genetic differentiation among populations (mtDNA control region sequences Φ_ST = -0.008; microsatellite loci F_ST = 0.003). A lack of evidence for regional or localized mtDNA haplotype clusters, or geographic clusters of microsatellite genotypes, reveals a pattern of high gene flow in P. ornatus throughout the South-East Asian Archipelago. This lack of genetic structure may be due to the oceanography-driven connectivity of the pelagic lobster larvae between spawning grounds in Papua New Guinea, the Philippines and, possibly, Indonesia. The connectivity cycle necessitates three generations. The lack of genetic structure of P. ornatus population in the South-East Asian archipelago has important implications for the sustainable management of this lobster in that the species within the region needs to be managed as one genetic stock.     

Contrasting effects of landscape features on genetic structure in different geographic regions in the ornate dragon lizard,Ctenophorus ornatus

Habitat fragmentation can have profound effects on the distribution of genetic variation within and between populations. Previously, we showed that in the ornate dragon lizard, Ctenophorus ornatus, lizards residing on outcrops that are separated by cleared agricultural land are significantly more isolated and hold less genetic variation than lizards residing on neighbouring outcrops connected by undisturbed native vegetation. Here, we extend the fine‐scale study to examine the pattern of genetic variation and population structure across the species' range. Using a landscape genetics approach, we test whether land clearing for agricultural purposes has affected the population structure of the ornate dragon lizard. We found significant genetic differentiation between outcrop populations (F_ST = 0.12), as well as isolation by distance within each geographic region. In support of our previous study, land clearing was associated with higher genetic divergences between outcrops and lower genetic variation within outcrops, but only in the region that had been exposed to intense agriculture for the longest period of time. No other landscape features influenced population structure in any geographic region. These results show that the effects of landscape features can vary across species' ranges and suggest there may be a temporal lag in response to contemporary changes in land use. These findings therefore highlight the need for caution when assessing the impact of contemporary land use practices on genetic variation and population structure.     

Colonization of the Philippines from Taiwan: a multi‐locus test of the biogeographic and phylogenetic relationships of isolated populations of shrews

Aim Colonization of the Philippines from Taiwan or neighbouring areas of the Asian mainland has been proposed as an important source of diversity for some plant and animal groups in the northern Philippines. Previous inferences, however, were based on taxonomic groupings, which sometimes fail to reflect phylogenetic history. Here, we test for colonization of the Philippines from the north in a group of shrews (Soricomorpha: Crocidura) using explicit inferences of evolutionary history. Location Southeast Asia. Methods We estimate the phylogenetic relationships of populations of shrews from Batan and Sabtang islands in the northern Philippines using DNA sequences from two mitochondrial genes and three nuclear loci. We employ topology tests to evaluate the possible relationships of these shrews to species from throughout Southeast Asia. Results We find conclusive evidence that shrews from Batan and Sabtang are closely related to Crocidura tanakae from Taiwan and additional specimens from the Asian mainland. Bayesian and frequentist topology tests using alignments of individual loci strongly reject any notion that shrews from Batan and Sabtang are part of the main Philippine radiation of Crocidura, indicating that the northernmost Philippine islands were almost certainly colonized by shrews from Taiwan or mainland Asia. Main conclusions Our results provide the first compelling evidence for colonization of the Philippine archipelago by a terrestrial vertebrate via a northern route. Invasion of the northern Philippines by shrews, however, did not lead to further range expansion to more southerly parts of the Philippines. This study, combined with previous results, documents that Crocidura colonized the Philippines at least three times. However, only one of these invasions led to in situ speciation and ubiquity across the archipelago. Our findings are part of a growing body of literature suggesting that oceanic archipelagos are often colonized multiple times by groups of closely related species, and occasionally from multiple sources.     

Structural changes to the uterus of the dwarf ornate wobbegong shark (Orectolobus ornatus) during pregnancy

Embryos of the viviparous dwarf ornate wobbegong shark (Orectolobus ornatus) develop without a placenta, unattached to the uterine wall of their mother. Here, we present the first light microscopy study of the uterus of O. ornatus throughout pregnancy. At the beginning of pregnancy, the uterine luminal epithelium and underlying connective tissue become folded to form uterine ridges. By mid to late pregnancy, the luminal surface is extensively folded and long luminal uterine villi are abundant. Compared to the nonpregnant uterus, uterine vasculature is increased during pregnancy. Additionally, as pregnancy progresses the uterine epithelium is attenuated so that there is minimal uterine tissue separating large maternal blood vessels from the fluid that surrounds developing embryos. We conclude that the uterus of O. ornatus undergoes an extensive morphological transformation during pregnancy. These uterine modifications likely support developing embryos via embryonic respiratory gas exchange, waste removal, water balance, and mineral transfer.     

Dogs Detect Larger Wind Energy Effects on Bats and Birds

As wind turbine-caused mortality of birds and bats increases with increasing wind energy capacity, accurate fatality estimates are needed to assess effects, identify collision factors, and formulate mitigation. Finding a larger proportion of collision victims reduces the magnitude of adjustment for the proportion not found, thus reducing opportunities for bias. We tested detection dogs in trials of bat and small-bird carcasses placed randomly in routine fatality monitoring at the Buena Vista and Golden Hills Wind Energy projects, California, USA, 2017. Of trial carcasses placed and confirmed available before next-day fatality searches, dogs detected 96% of bats and 90% of small birds, whereas humans at a neighboring wind project detected 6% of bats and 30% of small birds. At Golden Hills dogs found 71 bat fatalities in 55 searches compared to 1 bat found by humans in 69 searches within the same search plots over the same season. Dog detection rates of trial carcasses remained unchanged with distance from turbine, and dogs found more fatalities than did humans at greater distances from turbines. Patterns of fatalities found by dogs within search plots indicated 20% of birds and 4–14% of bats remained undetected outside search plots at Buena Vista and Golden Hills. Dogs also increased estimates of carcass persistence by finding detection trial carcasses that the trial administrator had erroneously concluded were removed. Compared to human searches, dog searches resulted in fatality estimates up to 6.4 and 2.7 times higher for bats and small birds, respectively, along with higher relative precision and >90% lower cost per fatality detection. © 2020 The Authors. The Journal of Wildlife Management published by Wiley Periodicals, Inc. on behalf of The Wildlife Society.     

The ectomycorrhizal fungus Amanita phalloides was introduced and is expanding its range on the west coast of North America

The deadly poisonous Amanita phalloides is common along the west coast of North America. Death cap mushrooms are especially abundant in habitats around the San Francisco Bay, California, but the species grows as far south as Los Angeles County and north to Vancouver Island, Canada. At different times, various authors have considered the species as either native or introduced, and the question of whether A. phalloides is an invasive species remains unanswered. We developed four novel loci and used these in combination with the EF1α and IGS loci to explore the phylogeography of the species. The data provide strong evidence for a European origin of North American populations. Genetic diversity is generally greater in European vs. North American populations, suggestive of a genetic bottleneck; polymorphic sites of at least two loci are only polymorphic within Europe although the number of individuals sampled from Europe was half the number sampled from North America. Endemic alleles are not a feature of North American populations, although alleles unique to different parts of Europe were common and were discovered in Scandinavian, mainland French, and Corsican individuals. Many of these endemic European haplotypes were found together at single sites in California. Early collections of A. phalloides dated prior to 1963 and annotated using sequences of the ITS locus proved to be different species of Amanita. The first Californian collections that we confirmed as A. phalloides were made from the Del Monte Hotel (now the Naval Postgraduate School) in Monterey, and on the campus of the University of California, Berkeley, in 1938 and in 1945. These historical data are used in combination with data on A. phalloides’ current distribution to estimate a rate of spread for A. phalloides in California. Many species of ectomycorrhizal (EM) fungi have been introduced across and among continents, but with this evidence, the death cap becomes the only known invasive EM fungus in North America.     

Characterization of microsatellite loci in polyploid Lavatera assurgentiflora ssp. assurgentiflora and ssp. glabra (Malvaceae)

Lavatera assurgentiflora (Malvaceae) is one of four species of the genus Lavatera native to California and Baja California. Two geographically defined subspecies are recognized: L. a. assurgentiflora on the northern islands and L. a. glabra on the southern islands. We isolated nine polymorphic microsatellite loci that amplify in both subspecies of L. assurgentiflora. Substantial levels of polymorphism were observed at many of the loci. Four loci exhibited more than 10 alleles, polymorphism information content ranged from 0.4 to 0.8, and up to six alleles were found in some individuals, supporting reports that these taxa are hexaploid. All loci also amplified in Lavatera lindsayi from Guadalupe Island, and we anticipate that they will cross‐amplify in other California Lavatera species as well.     

Population genetic history of the dreissenid mussel invasions: expansion patterns across North America

This study tests population genetic patterns across the Eurasian dreissenid mussel invasions of North America—encompassing the zebra mussel Dreissena polymorpha (1986 detection) and the quagga mussel D. rostriformis bugensis (detected in 1990, which now has largely displaced the former in the Great Lakes). We evaluate their source-spread relationships and invasion genetics using 9–11 nuclear microsatellite loci for 583 zebra mussels (21 sites) and 269 quagga mussels (12 sites) from Eurasian and North American range locations, with the latter including the Great Lakes, Mississippi River basin, Atlantic coastal waterways, Colorado River system, and California reservoirs. Additionally, mtDNA cytochrome b gene sequences are used to verify species identity. Our results indicate that North American zebra mussels originate from multiple non-native northern European populations, whereas North American quagga mussels trace to native estuaries in the Southern Bug and Dnieper Rivers. Invasive populations of both species show considerable genetic diversity and structure (zebra F _ST = 0.006–0.263, quagga F _ST = 0.008–0.267), without founder effects. Most newer zebra mussel populations have appreciable genetic diversity, whereas quagga mussel populations from the Colorado River and California show some founder effects. The population genetic composition of both species changed over time at given sites; with some adding alleles from adjacent populations, some losing them, and all retaining closest similarity to their original composition. Zebra mussels from Kansas and California appear genetically similar and assign to a possible origin from the St. Lawrence River, whereas quagga mussels from Nevada and California assign to a possible origin from Lake Ontario. These assignments suggest that overland colonization pathways via recreational boats do not necessarily reflect the most proximate connections. In conclusion, our microsatellite results comprise a valuable baseline for resolving present and future dreissenid mussel invasion pathways.     

Do Displays Send Information about Ornament Structure and Male Quality in the Ornate Tree Lizard,Urosaurus ornatus?

Displays can transmit information about ornament or male quality; however, few studies have simultaneously explored the relationship between displays, ornament and male quality within a single species. We quantified ornament morphology (five throat color morphs, throat area, and belly area), male quality (bite force, sprint speed, body condition, and body mass), display behavior [percent time displaying (PTD), number of pushups per display, and display duration], and movement behavior among males in a population of the ornate tree lizard, Urosaurus ornatus. Previous studies have shown that male U. ornatus are polymorphic in throat coloration and that morphs differ in behavioral aggression. Our study shows that blue throat morphs use 1.5 more pushups per display than other male color morphs, which suggests that throat color and display behavior act as backup signals for aggression. However, other data support the multiple messages hypothesis, and overall our data do not provide conclusive evidence for any one hypothesis. In addition, we show that body mass is positively related to both PTD and percent time moving and this relationship is independent of color morph. We also found that throat area, belly area, bite force, sprint speed, and body condition are unrelated to display behavior. This result highlights at least some discordance between display behavior, ornaments, and performance in U. ornatus and suggests that these traits may be evolving independently.     

Genetic Structure and Gene Flow in Elymus glaucus (blue wildrye): Implications for Native Grassland Restoration

Interest in using native grass species for restoration is increasing, yet little is known about the ecology and genetics of native grass populations or the spatial scales over which seed can be transferred and successfully grown. The purpose of this study was to investigate the genetic structure within and among populations of Elymus glaucus in order to make some preliminary recommendations for the transfer and use of this species in revegetation and restoration projects. Twenty populations from California, Oregon, and Washington were analyzed for allozyme genotype at 20 loci, and patterns of variation within and among populations were determined. Allozyme variation at the species level was high, with 80% of the loci polymorphic and an average expected heterozygosity (an index of genetic diversity) of 0.194. All but two of the populations showed some level of polymorphism. A high degree of population differentiation was found, with 54.9% of the variation at allozyme loci partitioned among populations (F_st= 0.549). A lesser degree of genetic differentiation among closely spaced subpopulations within one of the populations was also demonstrated (F_st= 0.124). Self-pollination and the patchy natural distribution of the species both likely contribute to the low level of gene flow (N_m= 0.205) that was estimated. Zones developed for the transfer of seed of commercial conifer species may be inappropriate for transfer of E. glaucus germplasm because conifer species are characterized by high levels of gene flow. Limited gene flow in E. glaucus can facilitate the divergence of populations over relatively small spatial scales. This genetic differentiation can be due to random genetic drift, localized selective pressures, or both. In order to minimize the chances of planting poorly adapted germplasm, seed of E. glaucus may need to be collected in close proximity to the proposed restoration site.     

ALLOZYME VARIATION WITHIN AND BETWEEN LASTHENIA MINOR AND ITS DERIVATIVE SPECIES,L. MARITIMA (ASTERACEAE)

Enzyme electrophoresis was employed to examine genetic variation at 20 loci in 16 populations of Lasthenia minor and 18 populations of its presumed derivative species L. maritima. The purposes of the study were to ascertain levels of genetic variation in each species, to assess how the variation at enzyme-coding genes is apportioned within and among populations of each species, and to determine the level of divergence between the two species. The two species are both diploid annuals, similar morphologically, and produce fertile F₁ hybrids when crossed. Lasthenia minor is self-incompatible and restricted to mainland California, whereas L. maritima is self-compatible and probably largely autogamous; it occurs on seabird rocks from central California to British Columbia. Mean genetic identities for pair-wise comparisons of populations of the two species are similar to values for populations of the same species, indicating they have not diverged at the 20 genes coding for soluble enzymes. Despite its more extensive geographical range, L. maritima exhibits only 50% of the genetic diversity of L. minor. The latter species apportions a greater amount of its diversity within populations, whereas the former harbors more diversity among populations than within them. This is probably a reflection of the different breeding systems of the two species. Six unique alleles were detected in L. minor, whereas only one novel allele was found in a single individual of L. maritima. The electrophoretic data are concordant with the suggestion that L. maritima is relatively recently derived from L. minor. The switch from outcrossing to selfing and selection of genotypes adapted to the chemically and physically unusual substrate on the seabird rocks are considered the critical steps in the evolution of L. maritima.     

Detection of Coccidioides immitis in Kern County, California, by multiplex PCR

Coccidioides immitis is a fungal human pathogen endemic to semiarid soils in southern California and Baja California (Mexico). Results of culture-dependent detection of C. immitis in the past indicated a spotty distribution and unreliable prediction of C. immitis growth sites and accumulation sites. In this project we investigated bulk soil samples for the presence of the pathogen in nonagricultural loamy soils at nine different locations around Bakersfield, Kern County, California, for almost 2 y (2008-2009). To detect the pathogen we used a multiplex PCR method with optimized soil handling and storage, DNA extraction procedure and PCR protocol. With this method we were able to detect C. immitis in 8.42% of our samples in 2008 (n = 285), mostly from early spring to early summer. In 2009 however the percentage of samples positive for C. immitis from the same sites declined to 2.68% (n = 261). We also were able to distinguish C. immitis growth sites from accumulation sites. One site close to a recreation area (Lake Webb, Buena Vista Lake Basin), not previously known to support the growth of C. immitis, was identified as a strong growth site of the fungus. The cultivation-independent method in this study together with soil parameters can be used to predict and confirm C. immitis growth sites and might be a valuable tool for public health institutions.     

Eight polymorphic microsatellite markers for kelp bass,Paralabax clathratus,amplified in three multiplex polymerase chain reaction sets

Kelp bass, Paralabrax clathratus, is an important sport fishery of California, USA and Baja, Mexico. Here we describe eight microsatellite loci developed for this species. Two loci were derived from known primers for other species in the family, Serranidae and six were developed anew using a clone enrichment protocol. Loci were arranged into three multiplex PCR (polymerase chain reaction) sets for fast throughput; 564 individuals from nine populations across the species’ range were genotyped. Polymorphism ranged from four to 47 alleles and all populations at all loci displayed Hardy–Weinberg and linkage equilibrium.     

Cross‐species comparison of microsatellite loci in the Culex pipiens complex and beyond

In the past, we have developed microsatellite loci from the two most common members of the Culex pipiens complex, Culex quinquefasciatus and Culex pipiens. Here we describe seven additional loci and present an extensive survey of a panel of 20 loci across most of the species and subspecies in the complex as well as in morphologically related species. Because we observed a high degree of polymorphism in the flanking regions, we designed new primers and surveyed multiple populations. We present alternate primers and discuss the cross‐species usefulness of these Culex microsatellite loci in a phylogenetic context.     

Genetic Diversity in Natural Populations of Arabidopsis thaliana (L.) Heynh. from Karelia

The genetic structure of ten natural populations of Arabidopsis thaliana (L.) Heynh. at eight isozyme loci was studied. The populations were located in the northern part of the species range, 200 km from the north to the south along the Onega Lake coast in Karelia. Considerable genetic diversity (P _99% = 43.7, H _obs = 0.003) was revealed that is not typical of populations of self-pollinating plant species. A direct correlation between the proportion of polymorphic loci and geographical latitude was shown (r = 0.68; P < 0.05). It is suggested that a high polymorphism level in Karelian Arabidopsis thaliana (L.) populations increasing from the south to the north is due to extreme environmental conditions in the northern part of the species range. The distribution of genetic diversity within and between populations is typical of self-pollinating species: the larger part of the total diversity resides among populations (G _ST = 0.583).     

The genetic population structure of lacustrine sockeye salmon, <Emphasis Type="Italic">Oncorhynchus nerka,</Emphasis> in Japan as the endangered species

Lacustrine sockeye salmon (Oncorhynchus nerka) are listed as an endangered species in Japan despite little genetic information on their population structure. In order to clarify the genetic diversity and structure of Japanese populations for evaluating on the bottleneck effect and an endangered species, we analyzed the ND5 region of mitochondrial DNA (mtDNA) and 45 single nucleotide polymorphisms (SNPs) in 640 lacustrine sockeye salmon in Japan and 80 anadromous sockeye salmon in Iliamna Lake of Alaska. The genetic diversity of the Japanese population in both mtDNA and SNPs was significantly less than that of the Iliamna Lake population. Moreover, all Japanese populations had SNP loci deviating from the HWE. In spite of low genetic diversity, the SNP analyses resulted that the Japanese population was significantly divided into three groups. These suggest that Japanese sockeye salmon populations should be protected as an endangered species and genetically disturbed by the hatchery program and transplantations.