Identifying factors driving sensitivity to fragmentation in forest breeding songbirds

Habitat loss and fragmentation are the greatest threats to biodiversity worldwide. Fragmentation impacts landscape configuration, resulting in a larger number of patches that are smaller in size and further apart from one another. Island biogeography and metapopulation theory predict populations in these remnant patches should be smaller, have higher extinction rates, and be less likely to receive immigrants from other populations. However, empirical data frequently do not conform with these theoretical predictions, leading to assertions that this model is too simplistic to describe distributions and dynamics of fragmented populations. However, others believe that landscape configuration effects have been poorly tested and modeled to date. In this dissertation, I use breeding bird data collected in a fragmented forest landscape to explore this lack of congruence between theory and reality. I first test the hypothesis that heterogeneity in the detectability of mobile species due to temporary emigration from sample sites can produce biased estimates of metapopulation rates. Next, I test for idiosyncrasies in the effects of forest loss and fragmentation on species belonging to different ecological trait groups. Lastly, I examine whether fragmentation actually reduces the functional connectivity of landscapes for species identified as fragmentation-sensitive. Dynamic occupancy models are popular for estimating metapopulation dynamic rates (colonization and extinction) from repeated presence/absence surveys of unmarked animals. This approach assumes closure among repeated samples within primary periods, allowing estimation of dynamic rates between these periods. However, the impact of temporary emigration (reversible changes in sampling availability) on dynamic rate estimates has not been tested. In Chapter 2, I use simulated data to investigate the degree to which temporary emigration could mislead researchers interested in quantifying metapopulation rates. I then compared results from three avian point count datasets to evaluate the likelihood that temporary emigration confounds estimates of dynamics for 19 species under a popular sampling protocol. Simulated experiments indicated that when secondary periods were open to temporary emigration, presence of dynamics was identified ≥ 95.1% of the time, and dynamic rate estimates were accurate. However, dynamic rates were biased when secondary periods were closed to temporary emigration. In empirical datasets, dynamic occupancy models had greater support than closed models for all species when secondary sampling periods occurred in immediate succession (i.e., 3 samples within 10 minutes); however, my results suggest that this is because these estimates were heavily influenced by temporary emigration. When counts within a primary period were separated by 24-48 hours, I found evidence of dynamics for less than half of these species. I recommend an alternative sampling approach that allows accurate estimation of dynamic rates when temporary emigration is of no interest, and introduce a novel model for estimating both processes simultaneously in rare cases where they are both of biological interest. Concern for violating the occupancy modeling closure assumption has led to widespread recommendations that samples within primary periods be conducted extremely close in time. However, these results indicate this is not the best approach when interest is in quantifying dynamic rates. While dynamic occupancy models provide estimates of ‘colonization’ and ‘extinction,’ these values do not inherently represent dynamics unless temporary emigration has been explicitly modeled or accounted for with sampling design. Naivete to this fact can result in incorrect conclusions about biological processes. While theory predicts that fragmentation should negatively influence biodiversity, empirical support of this idea is weak in terrestrial systems. However, tests of fragmentation effects are typically confounded with landscape composition and potentially obscured by imperfect detection. In Chapter 3, I used multi-species occupancy models and a mensurative experimental design to test competing hypotheses about how forest fragmentation influences distributions of breeding forest bird species and communities. During the breeding seasons of 2011-2013, we recorded over 80,000 bird detections in 202 forest fragments using a sampling design that isolated the effects of patch size per se from the effects of forest amount (2 km), edge, local vegetation, and sample area. I modeled the effects of these covariates on distributions of individual species categorized by ecological trait groups (i.e., forest, forest interior, or forest edge). Though my results indicated little effect of patch size on total species richness, increasing patch size tended to have a positive effect on interior species, and a negative effect on edge species. The effects of total forest amount were much more variable, and actually had a negative influence on many species, particularly cavity nesters. My results do not support theoretical predictions that forest patch size should positively influence bird species richness. However, composition of bird communities does shift toward edge species from interior species with decreasing patch size. Maintaining large forest patches is thus critical for supporting forest interior species, which tend to be of greater conservation concern. Maintenance of metapopulations requires movement of dispersers among resource patches. The degree to which a landscape facilitates or impedes such movements is defined as functional connectivity. Habitat fragmentation may reduce the functional connectivity of a landscape, but empirical linkages between distribution patterns and movement ability are lacking. In Chapter 4, I use experimental translocations to test whether forest fragmentation impedes movement of two species identified as fragmentation-sensitive in Chapter 3: Wood Thrush (Hylocichla mustelina) and Ovenbirds (Seiurus aurocapilla). I also tested for behavioral changes in translocated birds and evaluated whether fragmentation effects differed between behavioral modes. Over two breeding seasons, we translocated 35 Wood Thrush and 19 Ovenbirds (1-1.2 km) across landscapes spanning a fragmentation gradient and recorded their movement paths using VHF transmitters and receivers. Eighty-seven percent of individuals returned successfully, taking as long as 72.2 hours. Movement patterns of 96% of successful birds indicated two distinct behavioral modes: exploring, characterized by short, undirected movements and course reversals; and homing, characterized by large, fast steps towards their home territories. Forest composition and configuration had no effect on homing time or path straightness for either species. However, at a finer scale, I found that both preferred to take steps that minimized their exposure to non-forested gaps. My results demonstrate that movement limitation could drive or exacerbate fragmentation sensitivity for these birds. Further, while fragmentation effects did not differ between behavioral modes, my results highlight the need to link the dichotomous behaviors of translocated animals with natural movement processes. Despite this knowledge gap, results from our study suggest that maintaining contiguous habitat or corridors may improve functional connectivity for fragmentation-sensitive birds.Keywords: forest fragmentation, dispersal, habitat amount, dynamic occupancy models, edge effects, extinction, metapopulation, patch size, colonization, temporary emigration, island biogeography, translocation experiment, functional connectivity, gap crossing behavior, movement behavior, detection probability, closure assumption, community occupancy model, breeding bird, Pollock's robust desig

Response to fragmentation by avian communities is mediated by species traits

Aim The hypothesis that habitat fragmentation negatively influences biodiversity stems from island biogeography and metapopulation theory which predict negative impacts of decreasing patch size on richness and distribution patterns. Empirical support of this idea is weak in terrestrial systems, though tests of fragmentation effects are typically confounded with landscape composition and potentially obscured by imperfect detection. Here, we used multispecies occupancy models and a mensurative experimental design to test competing hypotheses about how forest fragmentation influences distributions of breeding forest bird species and communities. Location Southern Indiana, USA. Methods During the breeding seasons of 2011-2013, we recorded over 80,000 bird detections in 202 forest fragments using a sampling design that isolated the effects of patch size per se from the effects of forest amount within a 2 km radius, edge distance, local vegetation and sampling area. We modelled the effects of these covariates on distributions of individual species categorized by ecological trait groups (i.e., forest, forest interior or forest edge), and evaluated how forest loss and fragmentation impact species richness. Results Though our results indicated little effect of patch size on total species richness, decreasing patch size had a negative effect on interior species, and a positive effect on edge species. The effects of total forest amount were much more variable, and surprisingly had a negative influence on many species, particularly cavity nesters. Main conclusions Our results do not support theoretical predictions that forest patch size should positively influence bird species richness. However, composition of bird communities shifted towards edge species from interior species with decreasing patch size. Maintaining large forest patches is thus critical for supporting forest interior species, which tend to be of the greatest conservation concern

Method for Improving the Reliability of Sound Broadcast Systems Used in Ecological Research and Management

Automated sound broadcast systems have been used to address a variety of ecological questions, and show great potential as a management tool. Such systems need to be reliable because treatments are often applied in the absence of a human observer and system failure can cause methodological ambiguity. During the breeding seasons of 2012 and 2013, we used a sound broadcast system previously described by Farrell and Campomizzi (2011) in an experiment evaluating the use of post-breeding song in forest-bird habitat selection in southern Indiana, USA. This system incorporates a portable compact disc (CD) player where the play button is permanently depressed using manual compression so that when a timer connects an electrical current to the unit, the CD player automatically starts. Despite exhaustive efforts to find a reliable way to manually compress the play button on numerous CD player models, play button failure was the most significant source of broadcast system failure (88%) in 2012. We attempted to resolve this problem in 2013 by removing the need for manual compression and soldering the play button contact poles on each CD players' integrated circuit boards. Though we did experience broadcast system failures during < 5% of treatment periods in 2013, none of those were attributable to play button failure. By removing all possibility of failure from manual play button compression we improved our system reliability. Thus, soldering the CD player play button on such broadcast systems represents a methodological improvement that can be used by researchers and managers interested in sound broadcast.Keywords: Play button depression mechanism, CD player, Sound broadcast system, Momentary action pushbutton switch, Bird son

Extinction filters mediate the global effects of habitat fragmentation on animals

Habitat loss is the primary driver of biodiversity decline worldwide, but the effects of fragmentation (the spatial arrangement of remaining habitat) are debated. We tested the hypothesis that forest fragmentation sensitivity—affected by avoidance of habitat edges—should be driven by historical exposure to, and therefore species’ evolutionary responses to disturbance. Using a database containing 73 datasets collected worldwide (encompassing 4489 animal species), we found that the proportion of fragmentation-sensitive species was nearly three times as high in regions with low rates of historical disturbance compared with regions with high rates of disturbance (i.e., fires, glaciation, hurricanes, and deforestation). These disturbances coincide with a latitudinal gradient in which sensitivity increases sixfold at low versus high latitudes. We conclude that conservation efforts to limit edges created by fragmentation will be most important in the world’s tropical forests

SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues

Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types

A first update on mapping the human genetic architecture of COVID-19

peer reviewe

Hutchinson et al data

This file contains the data used in the empirical case study of our manuscript. The first three tabs contain site occupancy, survey-specific covariates, and site-specific covariates for our full (656 sites, 3 surveys) survey effort. The last three tabs contain site occupancy, survey-specific covariates, and site-specific covariates for the first 2 surveys from 55 randomly-selected sites (the reduced data set in the paper). Further information is available in the attached "ReadMe" file

Case Study Data

This file contains one row for each site visit (3) to each point count station (193) for each of the 19 species examined. Point count stations were 50 m radius circles, and we recorded a 1 in detection columns only when the species was detected inside that circle. As part of a separate project, point count stations were located on 12 different forest plots within 6 publicly-owned entities. We provide additional sampling details (e.g., Julian date, air temperature, wind speed) that were not used in the case study data analysis

Data from: Distinguishing distribution dynamics from temporary emigration using dynamic occupancy models

1. Dynamic occupancy models are popular for estimating dynamic distribution rates (colonization and extinction) from repeated presence/absence surveys of unmarked animals. This approach assumes closure among repeated samples within primary periods, allowing estimation of dynamic rates between these periods. However, the impact of temporary emigration (reversible changes in sampling availability) on dynamic rate estimates, has not been tested. 2. Using simulated data, we investigated the degree to which temporary emigration could mislead researchers interested in quantifying dynamics. We then compared results from three avian point count datasets to evaluate the likelihood that temporary emigration confounds estimates of dynamics for 19 species under a popular sampling protocol. 3. Simulated experiments indicated that when secondary periods were open to temporary emigration, presence of dynamics was correctly identified ≥ 95.1% of the time, and dynamic rate estimates were accurate. However, dynamic rate estimates were biased when secondary periods were closed to temporary emigration. In empirical datasets, dynamic occupancy models had greater support than closed models for all species when secondary sampling periods occurred in immediate succession (i.e., 3 samples within 10 minutes); however, our results suggest that this is because these estimates were heavily influenced by temporary emigration. When counts within a primary period were separated by 24-48 hours, we found evidence of dynamics for less than half of these species. We recommend an alternative sampling approach that allows accurate estimation of dynamic rates when temporary emigration is of no interest, and introduce a novel model for estimating both processes simultaneously in rare cases where they are both of biological interest. 4. Concern for violating the occupancy modeling closure assumption has led to widespread recommendations that samples within primary periods be conducted extremely close in time. However, this may not be the best approach when interest is in quantifying dynamic rates. While dynamic occupancy models provide estimates of ‘colonization’ and ‘extinction,’ these values do not inherently represent dynamics unless temporary emigration has been explicitly modeled, or accounted for with sampling design. Naiveté to this fact can result in incorrect conclusions about biological processes