Conservation genetics of the endangered San Francisco Bay endemic salt marsh harvest mouse (Reithrodontomys raviventris)

Statham, Mark J.; Aamoth, S.; Barthman–Thompson, Laureen; Estrella, Sarah; Fresquez, Susan; Hernández, Luís; Tertes, Rachel; Sacks, Benjamin N.

doi:10.1007/s10592-016-0843-4

Cited by 21 publications

(29 citation statements)

References 30 publications

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“…However, RERA is the only mammal species in the world that is entirely endemic to coastal marshes (Greenberg & Maldonado, ) and is found only in tidal marshes in SFB (Figure ). It currently occupies <25% of its historic range because of habitat fragmentation and loss, with >80% loss of historic wetland habitat in SFB (Statham et al, ). The northern subspecies ( R. r. halicoetes ) is found along San Pablo Bay, and the southern subspecies ( R. r. raviventris ) is found in South SFB with the subspecies divide somewhere in Central Bay (Shellhammer, ; Statham et al, ; USFWS, ).…”

Section: Methodsmentioning

confidence: 99%

Habitat of the endangered salt marsh harvest mouse (Reithrodontomys raviventris) in San Francisco Bay

Marcot

Woo

Thorne

et al. 2020

Ecology and Evolution

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Understanding habitat associations is vital for conservation of at-risk marsh-endemic wildlife species, particularly those under threat from sea level rise. We modeled environmental and habitat associations of the marsh-endemic, Federally endangered salt marsh harvest mouse (Reithrodontomys raviventris, RERA) and co-occurrence with eight associated small mammal species from annual trap data, 1998-2014, in six estuarine marshes in North San Francisco Bay, California. Covariates included microhabitat metrics of elevation and vegetation species and cover; and landscape metrics of latitude-longitude, distance to anthropogenic features, and habitat patch size. The dominant cover was pickleweed (Salicornia pacifica) with 86% mean cover and 37 cm mean height, and bare ground with about 10% mean cover. We tested 38 variants of Bayesian network (BN) models to determine covariates that best account for presence of RERA and of all nine small mammal species. Best models had lowest complexity and highest classification accuracy. Among RERA presence models, three best BN models used covariates of latitude-longitude, distance to paved roads, and habitat patch size, with 0% error of false presence, 20% error of false nonpresence, and 20% overall error. The all-species presence models suggested that within the pickleweed marsh environment, RERA are mostly habitat generalists. Accounting for presence of other species did not improve prediction of RERA. Habitat attributes compared between RERA and the next most frequently captured species, California vole (Microtus californicus), suggested substantial habitat overlap, with RERA habitat being somewhat higher in marsh elevation, greater in percent cover of the dominant plant species, closer to urban areas, further from agricultural areas, and, perhaps most significant, larger in continuous size of marsh patch. Findings will inform conservation management of the marsh environment for RERA by identifying best microhabitat elements, landscape attributes, and adverse interspecific interactions. K E Y W O R D SBayesian network models, California vole, habitat use, Microtus californicus, occupancy, Reithrodontomys raviventris, salt marsh harvest mouse, San Francisco Bay, San Pablo Bay, small mammal assemblage | 663 MARCOT eT Al.

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Section: Methodsmentioning

confidence: 99%

Habitat of the endangered salt marsh harvest mouse (Reithrodontomys raviventris) in San Francisco Bay

Marcot

Woo

Thorne

et al. 2020

Ecology and Evolution

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“…The southern subspecies ( R. r. raviventris ) primarily occupies the southern portion of the San Francisco Bay (Shellhammer ). The salt marsh harvest mouse is geographically restricted to these North‐ and South‐Bay salt marshes, and despite the relatively short geographic distances between them, there is significant genetic (Statham et al ) and morphological (Fisler ) differentiation between subspecies. In addition, both are federal and California state‐listed endangered species.…”

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confidence: 99%

“…The western harvest mouse occurs in a diversity of vegetation types and in San Francisco and associated bays, it overlaps the range of, and coexists with, both salt marsh harvest mouse subspecies (Fisler , Shellhammer , Webster and Jones , Bias and Morrison , Sustaita et al ). This presents a problem for identifying and monitoring salt marsh harvest mouse populations in the field because of difficulties distinguishing between some ambiguous individuals with intermediate morphology (Hooper , Fisler , Bias and Morrison , Statham et al ).…”

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confidence: 99%

“…Chromosomal (Hood et al ), allozyme (Nelson et al ), and molecular (Bell et al ; Brown ; Arellano et al , ) studies have demonstrated that the salt marsh harvest mouse is most closely related to the plains harvest mouse ( R. montanus ). Fisler () reported no evidence that salt marsh and western harvest mice interbreed in captivity, and both mitochondrial (Brown ) and nuclear (Statham et al ) DNA evidence do not support the existence of hybrids.…”

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confidence: 99%

“…The problem of salt marsh harvest mouse field identification is not restricted to the northern subspecies (Statham et al ). However, only the northern subspecies and western harvest mouse coexist throughout the Suisun Marsh study area, hence the imperative for distinguishing between these 2 taxa in particular.…”

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Distinguishing between northern salt marsh and western harvest mice

et al. 2018

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The northern subspecies of the salt marsh harvest mouse (Reithrodontomys raviventris halicoetes) is morphologically similar to the western harvest mouse (R. megalotis) with which it co-occurs in the Suisun Marsh, California, USA, and therefore they are difficult to distinguish in the field. The salt marsh harvest mouse is a federal and California state-listed endangered species, whereas the western harvest mouse has no special status. Thus, our objective was to identify the most effective field metrics that distinguish the species. First we identified a barcode of life and restriction fragment length polymorphism approach for genetically distinguishing between the species. Then we performed univariate tests to examine variation in standard external morphological traits within and between species, and found that differences between species were confounded by sex and age. We then used discriminant function analysis and multiple logistic regression (MLR) to find combinations of characters that resulted in the highest percentages of correct classification based on a data set of individuals with genetically verified species identity. The best model (MLR) correctly classified 90.1 AE 3.5% ( x AE SD) of individuals, though all approaches performed relatively poorly with smaller, ostensibly younger, mice. Therefore, tail length, body length, and tail diameter, if treated in a comprehensive multivariate context, can yield substantial accuracy for distinguishing between coexisting northern salt marsh and western harvest mice. Ó 2018 The Wildlife Society.KEY WORDS discriminant function analysis, field identification, multiple logistic regression, Reithrodontomys, salt marsh harvest mouse, Suisun Marsh, western harvest mouse.

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Application of lidar to assess the habitat selection of an endangered small mammal in an estuarine wetland environment

Hagani,

Takekawa,

Skalos

et al. 2024

Ecology and Evolution

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Light detection and ranging (lidar) has emerged as a valuable tool for examining the fine‐scale characteristics of vegetation. However, lidar is rarely used to examine coastal wetland vegetation or the habitat selection of small mammals. Extensive anthropogenic modification has threatened the endemic species in the estuarine wetlands of the California coast, such as the endangered salt marsh harvest mouse (Reithrodontomys raviventris; SMHM). A better understanding of SMHM habitat selection could help managers better protect this species. We assessed the ability of airborne topographic lidar imagery in measuring the vegetation structure of SMHM habitats in a coastal wetland with a narrow range of vegetation heights. We also aimed to better understand the role of vegetation structure in habitat selection at different spatial scales. Habitat selection was modeled from data compiled from 15 small mammal trapping grids collected in the highly urbanized San Francisco Estuary in California, USA. Analyses were conducted at three spatial scales: microhabitat (25 m2), mesohabitat (2025 m2), and macrohabitat (~10,000 m2). A suite of structural covariates was derived from raw lidar data to examine vegetation complexity. We found that adding structural covariates to conventional habitat selection variables significantly improved our models. At the microhabitat scale in managed wetlands, SMHM preferred areas with denser and shorter vegetation and selected for proximity to levees and taller vegetation in tidal wetlands. At the mesohabitat scale, SMHM were associated with a lower percentage of bare ground and with pickleweed (Salicornia pacifica) presence. All covariates were insignificant at the macrohabitat scale. Our results suggest that SMHM preferentially selected microhabitats with access to tidal refugia and mesohabitats with consistent food sources. Our findings showed that lidar can contribute to improving our understanding of habitat selection of wildlife in coastal wetlands and help to guide future conservation of an endangered species.

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Conservation genetics of the endangered San Francisco Bay endemic salt marsh harvest mouse (Reithrodontomys raviventris)

Cited by 21 publications

References 30 publications

Habitat of the endangered salt marsh harvest mouse (Reithrodontomys raviventris) in San Francisco Bay

Habitat of the endangered salt marsh harvest mouse (Reithrodontomys raviventris) in San Francisco Bay

Distinguishing between northern salt marsh and western harvest mice

Application of lidar to assess the habitat selection of an endangered small mammal in an estuarine wetland environment

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