Historic DNA reveals contemporary population structure results from anthropogenic effects, not pre-fragmentation patterns

Genetic diversity and shallow genetic differentiation of the endangered scaly-sided merganser Mergus squamatus

Examining patterns of genetic diversity are crucial for conservation planning on endangered species, while inferring the underlying process of recent anthropogenic habitat modifications in the context potential long-term demographic changes remains challenging. The globally endangered scaly-sided merganser (SSME), Mergus squamatus, is endemic to a narrow range in Northeast Asia, and its population has recently been contracted into two main breeding areas. Although low genetic diversity has been suggested in the Russian population, the genetic status and demographic history of these individuals have not been fully elucidated. We therefore examined the genetic diversity and structure of the breeding populations of the SSME and investigated the relative importance of historical and recent demographic changes to the present-day pattern of genetic diversity. Using 10 nuclear microsatellite (SSR) markers and mitochondrial DNA (mtDNA) control region sequences, we found limited female-inherited genetic diversity and a high level of nuclear genetic diversity. In addition, analysis of both markers consistently revealed significant but weak divergence between the breeding populations. Inconsistent demographic history parameters calculated from mtDNA and bottleneck analysis results based on SSR suggested a stable historical effective population size. By applying approximate Bayesian computation, it was estimated that populations started to genetically diverge from each other due to recent fragmentation events caused by anthropogenic effects rather than isolation during Last Glacial Maximum (LGM) and post-LGM recolonization. These results suggest that limited historical population size and shallow evolutionary history may be potential factors contributing to the contemporary genetic diversity pattern of breeding SSME populations. Conservation efforts should focus on protecting the current breeding habitats from further destruction, with priority given to both the Russian and Chinese population, as well as restoring the connected suitable breeding grounds.

Genetic divergence between isolated populations of the North Island New Zealand Rifleman (Acanthisitta chloris granti) implicates ancient biogeographic impacts rather than recent habitat fragmentation

This research investigates the extent and causal mechanisms of genetic population divergence in a poorly flighted passerine, the North Island Rifleman or Titipounamu (Acanthisitta chloris granti). While this species has a historically widespread distribution, anthropogenic forest clearance has resulted in a highly fragmented current distribution. We conducted analyses of mitochondrial DNA (COI and Control Region) and 12 nuclear DNA microsatellites to test for population divergence and estimate times of divergence. diyabc and biogeobears were then used to assess likely past dispersal scenarios based on both mtDNA and nDNA. The results reveal several significantly divergent lineages across the North Island of New Zealand and indicate that some populations have been isolated for extensive periods of time (0.7-4.9 mya). Modeling indicated a dynamic history of population connectivity, with a drastic restriction in gene flow between three geographic regions, followed by a more recent re-establishment of connectivity. Our analyses indicate the dynamic influence of key geological and climatological events on the distribution of genetic diversity in this species, including support for the genetic impact of old biogeographic boundaries such as the Taupo Line and Cockayne's Line, rather than recent anthropogenic habitat fragmentation. These findings present a rare example of an avian species with a genetic history more like that of flightless taxa and so provide new general insights into vicariant processes affecting populations of passerines with limited dispersal.

Spatiotemporal Genetic Diversity of Lions Reveals the Influence of Habitat Fragmentation across Africa

Direct comparisons between historical and contemporary populations allow for detecting changes in genetic diversity through time and assessment of the impact of habitat fragmentation. Here, we determined the genetic architecture of both historical and modern lions to document changes in genetic diversity over the last century. We surveyed microsatellite and mitochondrial genome variation from 143 high-quality museum specimens of known provenance, allowing us to directly compare this information with data from several recently published nuclear and mitochondrial studies. Our results provide evidence for male-mediated gene flow and recent isolation of local subpopulations, likely due to habitat fragmentation. Nuclear markers showed a significant decrease in genetic diversity from the historical (HE = 0.833) to the modern (HE = 0.796) populations, whereas mitochondrial genetic diversity was maintained (Hd = 0.98 for both). Although the historical population appears to have been panmictic based on nDNA data, hierarchical structure analysis identified four tiers of genetic structure in modern populations and was able to detect most sampling locations. Mitogenome analyses identified four clusters: Southern, Mixed, Eastern, and Western and were consistent between modern and historically sampled haplotypes. Within the last century, habitat fragmentation caused lion subpopulations to become more geographically isolated as human expansion changed the African landscape. This resulted in an increase in fine-scale nuclear genetic structure and loss of genetic diversity as lion subpopulations became more differentiated, whereas mitochondrial structure and diversity were maintained over time.

Howling from the past: historical phylogeography and diversity losses in European grey wolves

Genetic bottlenecks resulting from human-induced population declines make alarming symbols for the irreversible loss of our natural legacy worldwide. The grey wolf (Canis lupus) is an iconic example of extreme declines driven by anthropogenic factors. Here, we assessed the genetic signatures of 150 years of wolf persecution throughout the Western Palaearctic by high-throughput mitochondrial DNA sequencing of historical specimens in an unprecedented spatio-temporal framework. Despite Late Pleistocene bottlenecks, we show that historical genetic variation had remained high throughout Europe until the last several hundred years. In Western Europe, where wolves nearly got fully exterminated, diversity dramatically collapsed at the turn of the twentieth century and recolonization from few homogeneous relict populations induced drastic shifts of genetic composition. By contrast, little genetic displacement and steady levels of diversity were maintained in Eastern European regions, where human persecution had lesser effects on wolf demography. By comparing prehistoric, historic and modern patterns of genetic diversity, our study hence traces the timeframe and the active human role in the decline of the grey wolf, an emblematic yet controversial animal which symbolizes the complex relationship between human societies and nature conservation.

Genetic structure of brown pelicans (Pelecanus occidentalis) in the northern Gulf of Mexico in the context of human management and disturbance

Environmental disturbances, both natural and anthropogenic, have the capacity to substantially impact animal behavior and abundance, which can in turn influence patterns of genetic diversity and gene flow. However, little empirical information is available on the nature and degree of such changes due to the relative rarity of longitudinal genetic sampling of wild populations at appropriate intervals. Addressing this knowledge gap is therefore of interest to evolutionary biologists, policy makers, and managers. In the past half century, populations of the brown pelican (Pelecanus occidentalis) in the southeastern United States have been exposed to regional extirpations, translocations, colony losses, and oil spills, but potential impacts on genetic diversity and population structure remain unknown. To investigate the cumulative impacts of recent disturbances and management actions, we analyzed seven microsatellite loci using genetic samples collected from 540 nestlings across twelve pelican colonies from two time periods, corresponding to before (n = 305) and after (n = 235) the 2010 Deepwater Horizon oil spill. Pre-2010 populations in Texas were significantly differentiated from Louisiana, Alabama, and Florida populations to the east, with reintroduced populations in southeastern Louisiana having less genetic diversity than sites in Texas, consistent with a recent bottleneck. In contrast, there was no evidence of a geographic component to genetic structure among colonies sampled after the spill, consistent with increased dispersal among sites following the event. This pattern may be associated with reduced philopatry in response to colony abandonment in the areas most heavily impacted by the Deepwater Horizon event, though other factors (e.g., rehabilitation and translocation of oiled birds or colony loss due to erosion and tropical storms) were likely also involved. Future monitoring is necessary to determine if bottlenecks and loss of genetic variation are associated with the oil spill over time, and is recommended for other systems in which disturbance effects may be inferred via repeated genetic sampling.

European Colonization, Not Polynesian Arrival, Impacted Population Size and Genetic Diversity in the Critically Endangered New Zealand Kākāpō

Island endemic species are often vulnerable to decline and extinction following human settlement, and the genetic study of historical museum specimens can be useful in understanding these processes. The kākāpō (Strigops habroptilus) is a critically endangered New Zealand parrot that was formerly widespread and abundant. It is well established that both Polynesian and European colonization of New Zealand impacted the native avifauna, but the timeframe and severity of impacts have differed depending on species. Here, we investigated the relative importance of the 2 waves of human settlement on kākāpō decline, using microsatellites and mitochondrial DNA (mtDNA) to characterize recent kākāpō genetic and demographic history. We analyzed samples from 49 contemporary individuals and 54 museum specimens dating from 1884 to 1985. Genetic diversity decreased significantly between historical and contemporary kākāpō, with a decline in mean number of microsatellite alleles from 6.15 to 3.08 and in number of mtDNA haplotypes from 17 to 3. Modeling of demographic history indicated a recent population bottleneck linked to the period of European colonization (approximately 5 generations ago) but did not support a major decline linked to Polynesian settlement. Effective population size estimates were also larger for historical than contemporary kākāpō. Our findings inform contemporary kākāpō management by indicating the timeframe and possible cause of the bottleneck, which has implications for the management of extant genetic diversity. We demonstrate the broader utility of a historical perspective in understanding causes of decline and managing extinction risk in contemporary endangered species.

Conservation implications of the evolutionary history and genetic diversity hotspots of the snowshoe hare

With climate warming, the ranges of many boreal species are expected to shift northward and to fragment in southern peripheral ranges. To understand the conservation implications of losing southern populations, we examined range-wide genetic diversity of the snowshoe hare (Lepus americanus), an important prey species that drives boreal ecosystem dynamics. We analysed microsatellite (8 loci) and mitochondrial DNA sequence (cytochrome b and control region) variation in almost 1000 snowshoe hares. A hierarchical structure analysis of the microsatellite data suggests initial subdivision in two groups, Boreal and southwestern. The southwestern group further splits into Greater Pacific Northwest and U.S. Rockies. The genealogical information retrieved from mtDNA is congruent with the three highly differentiated and divergent groups of snowshoe hares. These groups can correspond with evolutionarily significant units that might have evolved in separate refugia south and east of the Pleistocene ice sheets. Genetic diversity was highest at mid-latitudes of the species' range, and genetic uniqueness was greatest in southern populations, consistent with substructuring inferred from both mtDNA and microsatellite analyses at finer levels of analysis. Surprisingly, snowshoe hares in the Greater Pacific Northwest mtDNA lineage were more closely related to black-tailed jackrabbits (Lepus californicus) than to other snowshoe hares, which may result from secondary introgression or shared ancestral polymorphism. Given the genetic distinctiveness of southern populations and minimal gene flow with their northern neighbours, fragmentation and loss of southern boreal habitats could mean loss of many unique alleles and reduced evolutionary potential.