Linking genetic kinship and demographic analyses to characterize dispersal:Methods and application to Blanding's turtle

Characterizing how frequently, and at what life stages and spatial scales, dispersal occurs can be difficult, especially for species with cryptic juvenile periods and long reproductive life spans. Using a combination of mark-recapture information, microsatellite genetic data, and demographic simulations, we characterize natal and breeding dispersal patterns in the long-lived, slow-maturing, and endangered Blanding's turtle (Emydoidea blandingii), focusing on nesting females. We captured and genotyped 310 individual Blanding's turtles (including 220 nesting females) in a central Wisconsin population from 2010 to 2013, with additional information on movements among 3 focal nesting areas within this population available from carapace-marking conducted from 2001 to 2009. Mark-recapture analyses indicated that dispersal among the 3 focal nesting areas was infrequent (<0.03 annual probability). Dyads of females with inferred first-order relationships were more likely to be found within the same nesting area than split between areas, and the proportion of related dyads declined with increasing distance among nesting areas. The observed distribution of related dyads for nesting females was consistent with a probability of natal dispersal at first breeding between nearby nesting areas of approximately 0.1 based on demographic simulations. Our simulation-based estimates of infrequent female dispersal were corroborated by significant spatial genetic autocorrelation among nesting females at scales of <500 m. Nevertheless, a lack of spatial genetic autocorrelation among non-nesting turtles (males and females) suggested extensive local connectivity, possibly mediated by male movements or long-distance movements made by females between terrestrial nesting areas and aquatic habitats. We show here that coupling genetic and demographic information with simulations of individual-based population models can be an effective approach for untangling the contributions of natal and breeding dispersal to spatial ecology

Finding the right coverage:The impact of coverage and sequence quality on single nucleotide polymorphism genotyping error rates

Restriction-enzyme-based sequencing methods enable the genotyping of thousands of single nucleotide polymorphism (SNP) loci in nonmodel organisms. However, in contrast to traditional genetic markers, genotyping error rates in SNPs derived from restriction-enzyme-based methods remain largely unknown. Here, we estimated genotyping error rates in SNPs genotyped with double digest RAD sequencing from Mendelian incompatibilities in known mother-offspring dyads of Hoffman's two-toed sloth (Choloepus hoffmanni) across a range of coverage and sequence quality criteria, for both reference-aligned and de novo-assembled data sets. Genotyping error rates were more sensitive to coverage than sequence quality and low coverage yielded high error rates, particularly in de novo-assembled data sets. For example, coverage &gt;= 5 yielded median genotyping error rates of &gt;= 0.03 and &gt;= 0.11 in reference-aligned and de novo-assembled data sets, respectively. Genotyping error rates declined to = 30, but remained &gt;= 0.04 in the de novo-assembled data sets. We observed approximately 10- and 13-fold declines in the number of loci sampled in the reference-aligned and de novo-assembled data sets when coverage was increased from &gt;= 5 to &gt;= 30 at quality score &gt;= 30, respectively. Finally, we assessed the effects of genotyping coverage on a common population genetic application, parentage assignments, and showed that the proportion of incorrectly assigned maternities was relatively high at low coverage. Overall, our results suggest that the trade-off between sample size and genotyping error rates be considered prior to building sequencing libraries, reporting genotyping error rates become standard practice, and that effects of genotyping errors on inference be evaluated in restriction-enzyme-based SNP studies.</p

The conundrum of agenda-driven science in conservation

Conservation biology is a value-laden discipline predicated on conserving biodiversity (Soulé 1985), a mission that does not always sit easily with objective science (Lackey 2007; Pielke 2007; Scott et al. 2007). While some encourage scientists to be responsible advocates for conservation (Garrard et al. 2016), others worry that objectivity in conservation research may suffer (Lackey 2007). At this time, we believe advocacy by scientists is essential for environmental conservation and, indeed, humanity. It is difficult to envision the state of our environment had scientists failed to encourage policy makers and the public to address emerging conservation problems. Nevertheless, conservation scientists must avoid misusing the scientific process to promote specific conservation outcomes (Wilholt 2009); doing so erodes the credibility of science and can produce undesirable consequences (Thomas 1992; Mills 2000; Rohr and McCoy 2010). We consider intentionally engaging in activities outside of professional norms to promote desired outcomes, as part of either the production or dissemination of science, to constitute “agenda-driven science”. The issue of advocacy-related bias in conservation science merits renewed discussion because conservation conflicts in an increasingly polarized world might tempt some to engage in agenda-driven science to “win” a conflict

Unexpected strong polygyny in the brown-throated three-toed sloth.

Promiscuous mating strategies are much more common than previously appreciated. So much so, that several authors have proposed that promiscuity is the "rule" rather than the exception in vertebrate mating systems. Decreasing species mobility and increasing habitat fragmentation have both been suggested to reduce the "polygyny potential" of the environment and promote other mating strategies like promiscuity in females. We explored the social and genetic mating system for one of the most sedentary extant mammals, the brown-throated three-toed sloth (Bradypus variegatus), within a highly fragmented Neotropical habitat. Surprisingly, we found that three-toed sloths were strongly polygynous, with males excluding male competitors from their core ranges, and exhibiting strong reproductive skew. Indeed, only 25% of all resident adult males sired offspring and one individual sired half of all sampled juveniles. Paradoxically, a sedentary life-history strategy seems to facilitate polygyny in fragmented landscapes because multiple females can persist within small patches of habitat, and be monopolized by a single male. Our work demonstrates that strong polygyny can arise in systems in which the polygyny potential should be extremely low, and other strategies, including promiscuity, would be favoured. Mating systems can be influenced by a multitude of factor and are dynamic, varying among taxa, over time, and across habitats; consequently, mating systems remain difficult to predict based on general ecological principles

Appendix A. Ratio of hatch-year to after-hatch-year individuals (R) and life history traits for 29 bird species used in the comparative analysis.

Ratio of hatch-year to after-hatch-year individuals (R) and life history traits for 29 bird species used in the comparative analysis

Appendix B. Survival estimates derived from mark–recapture analyses and life history traits of alcids used in comparative analysis.

Survival estimates derived from mark–recapture analyses and life history traits of alcids used in comparative analysis

Index Files

Index File

Data from: Genetic effects of landscape, habitat preference, and demography on three co-occurring turtle species

Expanding the scope of landscape genetics beyond the level of single species can help to reveal how species traits influence responses to environmental change. Multispecies studies are particularly valuable in highly threatened taxa, such as turtles, in which the impacts of anthropogenic change are strongly influenced by interspecific differences in life-history strategies, habitat preferences, and mobility. We sampled approximately 1500 individuals of three co-occurring turtle species across a gradient of habitat change (including varying loss of wetlands and agricultural conversion of upland habitats) in the Midwestern USA. We used genetic clustering and multiple regression methods to identify associations between genetic structure and permanent landscape features, past landscape composition, and landscape change in each species. Two aquatic generalists (the painted turtle, Chrysemys picta, and the snapping turtle Chelydra serpentina) both exhibited population genetic structure consistent with isolation-by-distance, modulated by aquatic landscape features. Genetic divergence for the more terrestrial Blanding's turtle (Emydoidea blandingii), on the other hand, was not strongly associated with geographic distance or aquatic features, and Bayesian clustering analysis indicated that many Emydoidea populations were genetically isolated. Despite long generation times, all three species exhibited associations between genetic structure and post-settlement habitat change, indicating that long generation times may not be sufficient to delay genetic drift resulting from recent habitat fragmentation. The concordances in genetic structure observed between aquatic species, as well as isolation in the endangered, long-lived Emydoidea, reinforce the need to consider both landscape composition and demographic factors in assessing differential responses to habitat change in co-occurring species