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We provide a century-scale view of small-mammal responses to global warming, without confounding effects of land-use change, by repeating Grinnell's early-20th century survey across a 3000-meter-elevation gradient that spans Yosemite National Park, California, USA. Using occupancy modeling to control for variation in detectability, we show substantial (~500 meters on average) upward changes in elevational limits for half of 28 species monitored, consistent with the observed ~3°C increase in minimum temperatures. Formerly low-elevation species expanded their ranges and high-elevation species contracted theirs, leading to changed community composition at mid- and high elevations. Elevational replacement among congeners changed because species' responses were idiosyncratic. Though some high-elevation species are threatened, protection of elevation gradients allows other species to respond via migration.

Resurveys of historical collecting localities have revealed range shifts, primarily leading edge expansions, which have been attributed to global warming. However, there have been few spatially replicated community-scale resurveys testing whether species' responses are spatially consistent. Here we repeated early twentieth century surveys of small mammals along elevational gradients in northern, central and southern regions of montane California. Of the 34 species we analysed, 25 shifted their ranges upslope or downslope in at least one region. However, two-thirds of ranges in the three regions remained stable at one or both elevational limits and none of the 22 species found in all three regions shifted both their upper and lower limits in the same direction in all regions. When shifts occurred, high-elevation species typically contracted their lower limits upslope, whereas low-elevation species had heterogeneous responses. For high-elevation species, site-specific change in temperature better predicted the direction of shifts than change in precipitation, whereas the direction of shifts by low-elevation species was unpredictable by temperature or precipitation. While our results support previous findings of primarily upslope shifts in montane species, they also highlight the degree to which the responses of individual species vary across geographically replicated landscapes.

Understanding how climatic change impacts biological diversity is critical to conservation. Yet despite demonstrated effects of climatic perturbation on geographic ranges and population persistence, surprisingly little is known of the genetic response of species. Even less is known over ecologically long time scales pertinent to understanding the interplay between microevolution and environmental change. Here, we present a study of population variation by directly tracking genetic change and population size in two geographically widespread mammal species (Microtus montanus and Thomomys talpoides) during late-Holocene climatic change. We use ancient DNA to compare two independent estimates of population size (ecological and genetic) and corroborate our results with gene diversity and serial coalescent simulations. Our data and analyses indicate that, with population size decreasing at times of climatic change, some species will exhibit declining gene diversity as expected from simple population genetic models, whereas others will not. While our results could be consistent with selection, independent lines of evidence implicate differences in gene flow, which depends on the life history strategy of species.

Invasive species can have complex invasion histories, harbor cryptic levels of diversity, and pose taxonomic problems for pest management authorities. Roof rats, Rattus rattus sensu lato, are common invasive pests of the San Francisco Bay Area in California, USA. They are a significant health risk and pest management efforts impose a large financial investment from public institutions and private individuals. Recent molecular genetic and taxonomic studies of black rats in their native range in Asia have shown that the species is a complex of two karyotypic forms and four mitochondrial genetic lineages that may represent four distinct species. We used mtDNA sequences and nuclear microsatellite variation to identify which mitochondrial lineages of the R. rattus group are present in the San Francisco Bay Area and to test for gene flow among them. We recovered specimens with mtDNA sequences representing two of the major mtDNA lineages of the R. rattus group. Microsatellite variation, however, was not structured in concordance with mtDNA lineages, suggesting a more complex history involving hybridization and introgression between these lineages. Although Aplin et al. ( 2011 ) and Lack et al. ( 2012 ) reported R. rattus Lineage II in North America, this is the first detailed examination of possible gene flow amongst lineages in this region.

The distribution of the black rat ( Rattus rattus ) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we first generate a de novo genome assembly of the black rat. We then sequence 67 ancient and three modern black rat mitogenomes, and 36 ancient and three modern nuclear genomes from archaeological sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of our newly reported sequences, together with published mitochondrial DNA sequences, confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling. ‘Archaeogenetic analysis of black rat remains reveals that this species was introduced into temperate Europe twice, in the Roman and medieval periods. This population turnover was likely associated with multiple historical and environmental factors.’

During mammal surveys at China Lake Naval Air Weapons Station in the Mojave Desert, we found California voles (Microtus californicus) infested with three flea species including the flea Stenistomera alpina. Collected near the eastern edge of the distribution of the vole and the western edge of the distribution of the flea, this is the first record of S. alpina on California voles, indeed on any Microtus species. Durante muestreos de mamíferos realizados en la Estación China Lake Naval Air Weapons ubicada en el desierto de Mojave, encontramos ratones de campo Microtus californicus infestados con tres especies de pulgas, incluyendo la especie Stenistomera alpina. Al haber sido colectados cerca del límite este del área de distribución de M. californicus y el límite oeste del área de distribución de S. alpina, este es el primer registro de S. alpina en M. californicus y en cualquier especie de Microtus.

During mammal surveys at China Lake Naval Air Weapons Station in the Mojave Desert, we found California voles (Microtus californiens) infested with three flea species including the flea Stenistomera alpina. Collected near the eastern edge of the distribution of the vole and the western edge of the distribution of the flea, this is the first record of S. alpina on California voles, indeed on any Microtus species.

The Owens Valley vole (Microtus californicus vallicola) exists in populations fragmented by natural aridity, land cultivation, highways and canals, and local urbanization. We used genetic analysis of six microsatellite DNA markers to investigate potential fragmentation, genetic drift, and geographic divergence of three populations distributed on the northern, southern, and central portions of the range. Our analyses found that the populations have similar levels of heterozygosity, no significant differences in allelic richness, and significant levels of genetic differentiation. With additional samples from intermediate locations, we would be able to better assess levels of gene flow among these populations. Our current results suggest that these populations do not necessarily require active management intervention.

Understanding population genetic structure and levels of genetic variation is critical for the conservation and management of imperiled populations, especially when reintroductions are planned. We used restriction-site associated DNA (RAD) sequencing to study the genetic diversity and evolutionary relationships of the endangered Amargosa vole and other closely related desert-dwelling California voles. Specifically, we sought to determine how Amargosa voles are related to other California voles, how genetic variation is partitioned among subpopulations in wild Amargosa voles, and how much genetic variation is captured within a captive insurance colony of Amargosa voles. Our multilocus nuclear dataset provides strong evidence that Amargosa voles are part of a northern clade of California voles. Amargosa voles have highly reduced genetic variation relative to other California voles, but do exhibit some sub-structure among sampled marshes. Captive Amargosa voles capture approximately half of the total genetic variation present in the wild Amargosa vole populations. We discuss the management implications of our findings in light of reintroductions planned for Amargosa voles. Our study highlights the utility of reduced representation genomic approaches, like RADseq, to resolve relationships among small populations that are difficult to study with traditional markers due to low genetic variation and few individuals left in the wild.

Temporal information on mammalian evolution allows testing of hypotheses about the mode of speciation and extinction, comparison of rates of evolution across taxa, and correlation of cladogenesis with important geological processes. Important insights can be made from combining data from fossils and molecules (DNA sequences), and relevant methods are expanding. When considering these methods, careful consideration should be given to features affecting time estimation (e.g., accuracy of tree construction, branch length estimation, taxonomic and genomic sampling, and sources of genetic and calibration errors). We report on the available methods that aid in evolutionary time estimation from molecular data and corresponding fossils. We recommend several steps to improve this process. First, we recommend using appropriate DNA substitution models to help correct DNA distance estimates and construct trees with more reliable branch lengths. Second, we recommend using multiple fossil calibration dates where possible. Third, in general, we recommend a conservative approach to time estimation by reporting inherent errors associated with genetic distances, calibration selection and application. In conclusion, temporal data derived from molecular clocks should be regarded in light of their dependence on paleontological information and their synergy with fossil data rather than competing with paleontological information. Thus, despite the varied sources of error, we encourage the extraction of time from molecular data with careful examination of potential biases.