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opennotspecifiedJul 2018View details →

FIG. 2 in Going with the Flow: Testing the Role of Habitat Isolation among Three Ecologically Divergent Darter Species

FIG. 2. Chart showing habitat characteristics of each darter species and predicted levels of gene flow between populations based on habitat variables. FST represents population differentiation, while AR represents allelic richness. Arrows pointing up indicate an increase, arrows pointing down a decrease, and horizontal arrows indicate moderate/intermediate levels. Illustrations were designed by Elizabeth Marchio (elizabeth. marchio@gmail.com; www.lizmarchio.com).

opennotspecifiedJul 2018View details →

FIG. 1 in Going with the Flow: Testing the Role of Habitat Isolation among Three Ecologically Divergent Darter Species

FIG. 1. Map of Pearl River including sampling sites for the three darter species. Ammocrypta beanii, Etheostoma swaini, and Percina nigrofasciata are represented by circles, squares, and diamonds, respectively. Map was generated using ArcGIS ArcMap 10.

opencc-zeroDec 2010View details →

Data from: Convergence and non-convergence in ecological, phenotypic, and genetic divergence across replicate population pairs of lake and stream stickleback

Convergent (or parallel) evolution provides strong evidence for a deterministic role of natural selection: similar phenotypes evolve when independent populations colonize similar environments. In reality, however, independent populations in similar environments always show some differences: some non-convergent evolution is present. It is therefore important to explicitly quantify the convergent and non-convergent aspects of trait variation, and to investigate the ecological and genetic explanations for each. We performed such an analysis for threespine stickleback (Gasterosteus aculeatus) populations inhabiting lake and stream habitats in independent watersheds. Morphological traits differed in the degree to which lake-stream divergence was convergent across watersheds. Some aspects of this variation were correlated with ecological variables related to diet, presumably reflecting the strength and specifics of divergent selection. Furthermore, a genetic scan revealed some markers that diverged between lakes and streams in many of the watersheds and some that diverged in only a few watersheds. Moreover, some of the lake-stream divergence in genetic markers was associated within some of the lake-stream divergence in morphological traits. Our results suggest that convergent evolution, and deviations from it, are primarily the result of natural selection, which corresponds in only some respect to the dichotomous habitat classifications frequently used in such studies.

opencc-zeroDec 2011View details →

Data from: Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua

The study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips in Midas cichlid fishes (the Amphilophus citrinellus species complex)—from two Great Lakes and two crater lakes in Nicaragua—to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next-generation sequencing technology, we characterize transcriptome-wide differential gene expression in the lips of wild-caught sympatric thick- and thin-lipped cichlids from all four instances of repeated thick-lip evolution. Six genes (apolipoprotein D, myelin-associated glycoprotein precursor, four-and-a-half LIM domain protein 2, calpain-9, GTPase IMAP family member 8-like and one hypothetical protein) are significantly underexpressed in the thick-lipped morph across all four lakes. However, other aspects of lips' gene expression in sympatric morphs differ in a lake-specific pattern, including the magnitude of differentially expressed genes (97-510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the older Great Lakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (δ13C and δ15N) differ between all sympatric morphs, with the greatest differentiation in the Great Lake Nicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick- and thin-lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution.

opencc-zeroJul 2021View details →

Data from: Divergent estimates of herd-wide caribou calf survival: ecological factors and methodological biases

Population monitoring is a critical part of effective wildlife management, but methods are prone to biases that can hinder our ability to accurately track changes in populations through time. Calf survival plays an important role in ungulate population dynamics and can be monitored using telemetry and herd composition surveys. These methods, however, are susceptible to unrepresentative sampling and violations of the assumption of equal detectability, respectively. Here we capitalized on 55 herd-wide estimates of woodland caribou (Rangifer tarandus caribou) calf survival in Newfoundland, Canada using telemetry (n = 1,175 calves) and 252 herd-wide estimates of calf:cow ratios (C:C) using herd composition surveys to investigate these potential biases. These data included 17 herd-wide estimates replicated from both methods concurrently (n = 448 calves and n =17 surveys) which we used to understand which processes and sampling biases contributed to disagreement between estimates of herd-wide calf survival. We used Cox proportional hazards models to determine if estimates of calf mortality risk were biased by the date a calf was collared. We also used linear mixed effects models to determine if estimates of C:C ratios were biased by survey date and herd size. We found that calves collared later in the calving season had a higher mortality risk and that C:C tended to be higher for surveys conducted later in the autumn. When we used these relationships to modify estimates of herd-wide calf survival derived from telemetry and herd composition surveys concurrently, we found that formerly disparate estimates of woodland caribou calf survival now overlapped (within a 95% confidence interval) in a majority of cases. Our case study highlights the potential of under-appreciated biases to impact our understanding of population dynamics and suggests ways that managers can limit the influence of these biases in the two widely applied methods for estimating herd-wide survival.

opencc-zeroJul 2019View details →

Data from: Genomics of rapid ecological divergence and parallel adaptation in four tidal marsh sparrows

Theory suggests that different taxa having colonized a similar, challenging environment will show parallel or lineage-specific adaptations to shared selection pressures, but empirical examples of parallel evolution in independent taxa are exceedingly rare. We employed comparative genomics to identify parallel and lineage-specific responses to selection within and among four species of North American sparrows that represent four independent, post-Pleistocene colonization events by an ancestral, upland subspecies and a derived salt marsh specialist. We identified multiple cases of parallel adaptation in these independent comparisons following salt marsh colonization, including selection on twelve candidate genes linked to osmoregulation. In addition to detecting shared genetic targets of selection across multiple comparisons, we found many novel, species-specific signatures of selection, including evidence of selection on loci associated with both physiological and behavioral mechanisms of osmoregulation. Demographic reconstructions of all four species highlighted their recent divergence and small effective population sizes, as expected given their rapid radiation into saline environments. Our results highlight the interplay of both shared and lineage-specific selection pressures in the colonization of a biotically and abiotically challenging habitat and confirm theoretical expectations that steep environmental clines can drive repeated and rapid evolutionary diversification in birds.

Figure 6. Identity test between L. laeta and L in Ecological niche divergence between the brown recluse spiders Loxosceles laeta and L. surca (Sicariidae) in Chile

Figure 6. Identity test between L. laeta and L. surca in Chile. The expected niche area is significantly out of the observed niche between them.

Figure 4 in Ecological niche divergence between the brown recluse spiders Loxosceles laeta and L. surca (Sicariidae) in Chile

Figure 4. Environmental suitability map for Loxosceles surca and Loxosceles laeta under Maxent algorithm. Colours represent different ranges of probabilities of presence (high probability: 0.75– 1.0). (a) Potential distribution of Loxosceles surca. (b) Potential distribution of Loxosceles laeta.

Figure 5 in Ecological niche divergence between the brown recluse spiders Loxosceles laeta and L. surca (Sicariidae) in Chile

Figure 5. Precipitations and annual mean temperatures both Loxosceles laeta and Loxosceles surca records. (a) Histogram of the frequency of precipitation of warmest quarter period, constructed from the known distribution of both species. (b) Histogram of the frequency of annual mean temperature, constructed from the known distribution of both species.

Figure 1 in Ecological niche divergence between the brown recluse spiders Loxosceles laeta and L. surca (Sicariidae) in Chile

Figure 1. Location records for two species of Loxosceles showing the range overlap in northern of Chile; L. laeta (blue circles) and L. surca (red triangles).

Figure 2 in Ecological niche divergence between the brown recluse spiders Loxosceles laeta and L. surca (Sicariidae) in Chile

Figure 2. Loxosceles surca in northern of Chile. (a) Habitat where the spiders were found. (b) Live female specimen of the Loxosceles surca, Altos de Pica, Chile. (Photography: William H. Piel).

Figure 3 in Ecological niche divergence between the brown recluse spiders Loxosceles laeta and L. surca (Sicariidae) in Chile

Figure 3. Maximum likelihood phylogeny of an alignment of COI and 28S sequences from Loxosceles species. The digits by each clade indicate percent bootstrap support based on 1,000 replicates. The species groups, as delineated by Gertsch (1967), are indicated by boxes enclosing clades. Continental biogeographic history is estimated using common-sense inference based on contemporary species distributions and is indicated in the figure using branch colours.

opencc-by-4.0May 2023View details →

Forest Types Show Divergent Biophysical Responses After Fire: Challenges to Ecological Modeling

<p>Datasets and scripts (MATLAB and R) used to document patterns of post-fire biophysical dynamics in seven forest types and 21 Level III ecoregions of the western United States.</p>