Can demographic histories explain long-term isolation and recent pulses of asymmetric gene flow between highly divergent grey fox lineages?

Secondary contact zones between deeply divergent, yet interfertile, lineages provide windows into the speciation process. North American grey foxes (Urocyon cinereoargenteus) are divided into western and eastern lineages that diverged approximately 1 million years ago. These ancient lineages currently hybridize in a relatively narrow zone of contact in the southern Great Plains, a pattern more commonly observed in smaller-bodied taxa, which suggests relatively recent contact after a long period of allopatry. Based on local ancestry inference with whole-genome sequencing (n = 43), we identified two distinct Holocene pulses of admixture. The older pulse (500–3500 YBP) reflected unidirectional gene flow from east to west, whereas the more recent pulse (70–200 YBP) of admixture was bi-directional. Augmented with genotyping-by-sequencing data from 216 additional foxes, demographic analyses indicated that the eastern lineage declined precipitously after divergence, remaining small throughout most of the late Pleistocene, and expanding only during the Holocene. Genetic diversity in the eastern lineage was highest in the southeast and lowest near the contact zone, consistent with a westward expansion. Concordantly, distribution modelling indicated that during their isolation, the most suitable habitat occurred far east of today\u27s contact zone or west of the Great Plains. Thus, long-term isolation was likely caused by the small, distant location of the eastern refugium, with recent contact reflecting a large increase in suitable habitat and corresponding demographic expansion from the eastern refugium. Ultimately, long-term isolation in grey foxes may reflect their specialized bio-climatic niche. This system presents an opportunity for future investigation of potential pre- and post-zygotic isolating mechanisms

Genomic analyses of gray fox lineages suggest ancient divergence and secondary contact in the southern Great Plains

The gray fox (Urocyon cinereoargenteus) lineage diverged from all other extant canids at their most basal node and is restricted to the Americas. Previous mitochondrial analysis from coastal populations identified deeply divergent (up to 1 Mya) eastern and western lineages that predate most intraspecific splits in carnivores. We conducted genotyping by sequencing and mitochondrial analysis on gray foxes sampled across North America to determine geographic concordance between nuclear and mitochondrial contact zones and divergence times. We also estimated the admixture within the contact zone between eastern and western gray foxes based on nuclear DNA. Both datasets confirmed that eastern and western lineages met in the southern Great Plains (i.e. Texas and Oklahoma), where they maintained high differentiation. Admixture was generally low, with the majority of admixed individuals carrying \u3c10% ancestry from the other lineage. Divergence times confirmed a mid-Pleistocene split, similar to the mitochondrial estimates. Taken together, findings suggest gray fox lineages represent an ancient divergence event, far older than most intraspecific divergences in North American carnivores. Low admixture may reflect a relatively recent time since secondary contact (e.g. post-Pleistocene) or, alternatively, ecological or reproductive barriers between lineages. Though further research is needed to disentangle these factors, our genomic investigation suggests species-level divergence exists between eastern and western gray fox lineages

Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest

Background Halyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species’ feeding and habitat traits, defining potential targets for pest management strategies. Results Analysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely support H. halys’ capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications. Conclusions Availability of the H. halys genome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls

Genetic diversity, population structure, and demographic history of the Hawaiʻi akepa

Thesis (M.S.)--University of Hawaii at Manoa, 2007.Includes bibliographical references (leaves 51-62).viii, 62 leaves, bound 29 cmAs a result of disease, habitat destruction, and other anthropogenic factors, the Hawaii Akepa (Loxops coccineus coccineus) currently occupies less than 10% of its original range and exists in five widely separated populations, raising concerns about what effect such reduction and fragmentation has had on the connectivity and diversity of Akepa populations. In this study, both historical and contemporary samples were utilized to assess genetic diversity and structure in this endangered Hawaiian honeycreeper. Sequence data from ND2, control region, and two nuclear introns were obtained from three of the five current populations, and control region sequence data were obtained from museum specimens collected over 100 years ago throughout the historical range of the bird. Results indicate that despite recent declines and fragmentation, genetic diversity has not yet been lost. No clear phylogeographic breaks were observed across the historical range of Akepa, but rather genetic differentiation was modest and seemed to follow a pattern of isolation-by-distance. Low levels of differentiation between the contemporary populations observed with mtDNA but not nuclear sequences indicate that not much divergence, if any. has occurred post-fragmentation. Rather, the present structure seen likely reflects historical isolation-by-distance. Ironically, this declining species exhibits the genetic signal of an expanding population, demonstrating that earlier demographic events are outweighing the effects of recent changes in population size, and genetic estimates of N., though crude, suggest Hawaii Akepa were at least an order of magnitude more abundant prior to the decline

Repro Measures

Provides Data on the reproductive effort and succes

Data from: Pleistocene and ecological effects on continental-scale genetic differentiation in the bobcat (Lynx rufus)

The potential for widespread, mobile species to exhibit genetic structure without clear geographic barriers is a topic of growing interest. Yet the patterns and mechanisms of structure – particularly over broad spatial scales – remain largely unexplored for these species. Bobcats occur across North America and possess many characteristics expected to promote gene flow. To test whether historical, topographic, or ecological factors have influenced genetic differentiation in this species, we analyzed 1 KB mtDNA sequence and 15 microsatellite loci from over 1700 samples collected across its range. The primary signature in both marker types involved a longitudinal cline with a sharp transition, or suture zone, occurring along the Great Plains. Thus, the data distinguished bobcats in the eastern U.S. from those in the western half, with no obvious physical barrier to gene flow. Demographic analyses supported a scenario of expansion from separate Pleistocene refugia, with the Great Plains representing a zone of secondary contact. Substructure within the two main lineages likely reflected founder effects, ecological factors, anthropogenic/topographic effects, or a combination of these forces. Two prominent topographic features, the Mississippi River and Rocky Mountains, were not supported as significant genetic barriers. Ecological regions and environmental correlates explained a small but significant proportion of genetic variation. Overall, results implicate historical processes as the primary cause of broad-scale genetic differentiation, but contemporary forces seem to also play a role in promoting and maintaining structure. Despite the bobcat’s mobility and broad niche, large-scale landscape changes have contributed to significant and complex patterns of genetic structure

Offspring Size Data

Provides data on liveborn offspring siz

Data from: Effects of early nutritional stress on physiology, life-histories and their trade-offs in a model ectothermic vertebrate

Early-life experiences can have far-reaching consequences for phenotypes into adulthood. The effect of early-life experiences on fitness, particularly under adverse conditions, is mediated by resource allocation to particular life-history traits. We examined the effects of early-life food restriction on growth, adult body size, physiology and reproduction in the checkered garter snake, Thamnophis marcianus. Animals were placed on one of two early-life diet treatments: normal-diet (approximating ad libitum feeding) or low-diet (restricted to 20% of body mass in food weekly). At 15 weeks of age low-diet animals were switched to the normal-diet treatment. Individuals fed a restricted diet showed reduced growth rates, depressed immunocompetence and a heightened glucocorticoid response. Once food restriction was lifted, animals that experienced nutritional stress early in life (low-diet) caught up to the normal-diet group by increasing their growth, and were able to recover from the negative effects of nutritional stress on physiology (immune function and stress response). Growth restriction and the subsequent allocation of resources into increasing growth rates, however, had a negative effect on fitness. Mating success was reduced in low-diet males, while low-diet females gave birth to smaller offspring. Our study demonstrates both immediate and long-term effects of nutritional stress on physiology and growth, reproduction, and trade-offs among them

Data from: Effects of early nutritional stress on physiology, life-histories and their trade-offs in a model ectothermic vertebrate

Early-life experiences can have far-reaching consequences for phenotypes into adulthood. The effect of early-life experiences on fitness, particularly under adverse conditions, is mediated by resource allocation to particular life-history traits. We examined the effects of early-life food restriction on growth, adult body size, physiology and reproduction in the checkered garter snake, Thamnophis marcianus. Animals were placed on one of two early-life diet treatments: normal-diet (approximating ad libitum feeding) or low-diet (restricted to 20% of body mass in food weekly). At 15 weeks of age low-diet animals were switched to the normal-diet treatment. Individuals fed a restricted diet showed reduced growth rates, depressed immunocompetence and a heightened glucocorticoid response. Once food restriction was lifted, animals that experienced nutritional stress early in life (low-diet) caught up to the normal-diet group by increasing their growth, and were able to recover from the negative effects of nutritional stress on physiology (immune function and stress response). Growth restriction and the subsequent allocation of resources into increasing growth rates, however, had a negative effect on fitness. Mating success was reduced in low-diet males, while low-diet females gave birth to smaller offspring. Our study demonstrates both immediate and long-term effects of nutritional stress on physiology and growth, reproduction, and trade-offs among them