Past climate change drives current genetic structure of an endangered freshwater mussel species

Historical‐to‐recent climate change and anthropogenic disturbance affect species distributions and genetic structure. The Rio Grande watershed of the United States and Mexico encompasses ecosystems that are intensively exploited, resulting in substantial degradation of aquatic habitats. While significant anthropogenic disturbances in the Rio Grande are recent, inhospitable conditions for freshwater organisms likely existed prior to such disturbances. A combination of anthropogenic and past climate factors may contribute to current distributions of aquatic fauna in the Rio Grande basin. We used mitochondrial DNA and 18 microsatellite loci to infer evolutionary history and genetic structure of an endangered freshwater mussel, Popenaias popeii, throughout the Rio Grande drainage. We estimated spatial connectivity and gene flow across extant populations of P. popeii and used ecological niche models (ENMs) and approximate Bayesian computation (ABC) to infer its evolutionary history during the Pleistocene. structure results recovered regional and local population clusters in the Rio Grande. ENMs predicted drastic reductions in suitable habitat during the last glacial maximum. ABC analyses suggested that regional population structure likely arose in this species during the mid‐to‐late Pleistocene and was followed by a late Pleistocene population bottleneck in New Mexico populations. The local population structure arose relatively recently, perhaps due to anthropogenic factors. Popenaias popeii, one of the few freshwater mussel species native to the Rio Grande basin, is a case study for understanding how both geological and anthropogenic factors shape current population genetic structure. Conservation strategies for this species should account for the fragmented nature of contemporary populations.     

Islands within islands: two montane palaeo‐endemic birds impacted by recent anthropogenic fragmentation

Anthropogenic habitat fragmentation of species that live in naturally patchy metapopulations such as mountaintops or sky islands experiences two levels of patchiness. Effects of such multilevel patchiness on species have rarely been examined. Metapopulation theory suggests that patchy habitats could have varied impacts on persistence, dependent on differential migration. It is not known whether montane endemic species, evolutionarily adapted to natural patchiness, are able to disperse between anthropogenic fragments at similar spatial scales as natural patches. We investigated historic and contemporary gene flow between natural and anthropogenic patches across the distribution range of a Western Ghats sky‐island‐endemic bird species complex. Data from 14 microsatellites for 218 individuals detected major genetic structuring by deep valleys, including one hitherto undescribed barrier. As expected, we found strong effects of historic genetic differentiation across natural patches, but not across anthropogenic fragments. Contrastingly, contemporary differentiation (D_PS) was higher relative to historic differentiation (F_ST) in anthropogenic fragments, despite the species’ ability to historically traverse shallow valleys. Simulations of recent isolation resulted in high D_PS/F_ST values, confirming recent isolation in Western Ghats anthropogenic fragments and also suggesting that this ratio can be used to identifying recent fragmentation in the context of historic connectedness. We suggest that in this landscape, in addition to natural patchiness affecting population connectivity, anthropogenic fragmentation additionally impacts connectivity, making anthropogenic fragments akin to islands within natural islands of montane habitat, a pattern that may be recovered in other sky‐island systems.     

Anthropogenic fragmentation may not alter pre‐existing patterns of genetic diversity and differentiation in perennial shrubs

Many plant species have pollination and seed dispersal systems and evolutionary histories that have produced strong genetic structuring. These genetic patterns may be consistent with expectations following recent anthropogenic fragmentation, making it difficult to detect fragmentation effects if no prefragmentation genetic data are available. We used microsatellite markers to investigate whether severe habitat fragmentation may have affected the structure and diversity of populations of the endangered Australian bird‐pollinated shrub Grevillea caleyi R.Br., by comparing current patterns of genetic structure and diversity with those of the closely related G. longifolia R.Br. that has a similar life history but has not experienced anthropogenic fragmentation. Grevillea caleyi and G. longifolia showed similar and substantial population subdivision at all spatial levels (global F′_ST = 0.615 and 0.454; S_p = 0.039 and 0.066), marked isolation by distance and large heterozygous deficiencies. These characteristics suggest long‐term effects of inbreeding in self‐compatible species that have poor seed dispersal, limited connectivity via pollen flow and undergo population bottlenecks because of periodic fires. Highly structured allele size distributions, most notably in G. caleyi, imply historical processes of drift and mutation were important in isolated subpopulations. Genetic diversity did not vary with population size but was lower in more isolated populations for both species. Through this comparison, we reject the hypothesis that anthropogenic fragmentation has impacted substantially on the genetic composition or structure of G. caleyi populations. Our results suggest that highly self‐compatible species with limited dispersal may be relatively resilient to the genetic changes predicted to follow habitat fragmentation.     

Comparative biogeography reveals differences in population genetic structure of five species of stream fishes

The distribution of genetic variation in Texas stream fishes has been shaped by a complex mix of historical and anthropogenic factors. Although Texas was not glaciated during the Pleistocene, the rise in sea level following this epoch isolated formerly connected drainages. More recently, the construction of dams, modifications of stream systems, and the release of commercially raised fish have influenced the patterns of genetic diversity. To examine how these different factors have impacted Texas stream fishes, we compared the genetic structure of five species of fish spanning two families and inhabiting two adjacent drainages: Lepomis megalotis, Lepomis cyanellus, Cyprinella lutrensis, Cyprinella venusta, and Campostoma anomalum. Our analyses of the mitochondrial D‐Loop show that genetic patterns differ strongly across species. A phylogeographical split between the Brazos and Trinity drainages was seen in conspecific populations of Lepomis species and is probably the result of the historical separation of these river systems. In contrast, contemporary ecological and anthropogenic factors, such as the desiccation of streams during summer, and the translocation of bait fish, appear to have a stronger influence on the genetic patterns in the remaining species. The contrasting results demonstrate the importance of using a multi‐species, comparative approach for landscape genetic studies as single species patterns may not be representative of others and thus may obscure differential effects of historical versus recent events as well as natural versus anthropogenic forces. By comparing closely related species that differ in their life history and economic importance it may be possible to disentangle the relative roles of historical, intrinsic, and anthropogenic influences on different organisms within a region. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ??, ??–??.     

Fine‐scale genetic structure and flowering output of the seagrass Enhalus acoroides undergoing disturbance

Seagrass are under great stress in the tropical coast of Asia, where Enhalus acoroides is frequently the dominant species with a large food web. Here, we investigate the question of the fine‐scale genetic structure of this ecologically important foundation species, subject to severe anthropogenic disturbance in China. The genetic structure will illuminate potential mechanisms for population dynamics and sustainability, which are critical for preservation of biodiversity and for decision‐making in management and restoration. We evaluated the fine‐scale spatial genetic structure (SGS) and flowering output of E. acoroides, and indirectly estimated the relative importance of sexual versus asexual reproduction for population persistence using spatial autocorrelation analysis. Results reveal high clonal diversity for this species, as predicted from its high sexual reproduction output. The stronger Sp statistic at the ramet‐level compared with genet‐level indicates that clonality increases the SGS pattern for E. acoroides. Significant SGS at the genet‐level may be explained by the aggregated dispersal of seed/pollen cohorts. The estimated gene dispersal variance suggests that dispersal mediated by sexual reproduction is more important than clonal growth in this study area. The ongoing anthropogenic disturbance will negatively affect the mating pattern and the SGS patterns in the future due to massive death of shoots, and less frequency of sexual reproduction.     

Genetic variation in an ephemeral mudflat species: The role of the soil seed bank and dispersal in river and secondary anthropogenic habitats

Many ephemeral mudflat species, which rely on a soil seed bank to build up the next generation, are endangered in their natural habitat due to the widespread regulation of rivers. The aim of the present study was to elucidate the role of the soil seed bank and dispersal for the maintenance of genetic diversity in populations of near‐natural river habitats and anthropogenic habitats created by traditional fish farming practices using Cyperus fuscus as a model. Using microsatellite markers, we found no difference in genetic diversity levels between soil seed bank and above‐ground population and only moderate differentiation between the two fractions. One possible interpretation is the difference in short‐term selection during germination under specific conditions (glasshouse versus field) resulting in an ecological filtering of genotypes out of the reservoir in the soil. River populations harbored significantly more genetic diversity than populations from the anthropogenic pond types. We suggest that altered levels and patterns of dispersal together with stronger selection pressures and historical bottlenecks in anthropogenic habitats are responsible for the observed reduction in genetic diversity. Dispersal is also supposed to largely prohibit genetic structure across Europe, although there is a gradient in private allelic richness from southern Europe (high values) to northern, especially north‐western, Europe (low values), which probably relates to postglacial expansion out of southern and/or eastern refugia.     

Phylogeography of noble crayfish (Astacus astacus) reveals multiple refugia

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Habitat fragmentation in coastal southern California disrupts genetic connectivity in the cactus wren (Campylorhynchus brunneicapillus)

Achieving long‐term persistence of species in urbanized landscapes requires characterizing population genetic structure to understand and manage the effects of anthropogenic disturbance on connectivity. Urbanization over the past century in coastal southern California has caused both precipitous loss of coastal sage scrub habitat and declines in populations of the cactus wren (Campylorhynchus brunneicapillus). Using 22 microsatellite loci, we found that remnant cactus wren aggregations in coastal southern California comprised 20 populations based on strict exact tests for population differentiation, and 12 genetic clusters with hierarchical Bayesian clustering analyses. Genetic structure patterns largely mirrored underlying habitat availability, with cluster and population boundaries coinciding with fragmentation caused primarily by urbanization. Using a habitat model we developed, we detected stronger associations between habitat‐based distances and genetic distances than Euclidean geographic distance. Within populations, we detected a positive association between available local habitat and allelic richness and a negative association with relatedness. Isolation‐by‐distance patterns varied over the study area, which we attribute to temporal differences in anthropogenic landscape development. We also found that genetic bottleneck signals were associated with wildfire frequency. These results indicate that habitat fragmentation and alterations have reduced genetic connectivity and diversity of cactus wren populations in coastal southern California. Management efforts focused on improving connectivity among remaining populations may help to ensure population persistence.     

Genetic diversity of Andean Polylepis (Rosaceae) woodlands and inferences regarding their fragmentation history

There is a long‐standing debate on whether the occurrence of the iconic high‐Andes Polylepis woodlands as small and isolated fragments is of natural or anthropogenic origin. We make inferences regarding the fragmentation history based on both a new population genetic study on P. besseri and a synthesis of available studies on the population genetics of Polylepis woodlands. We infer the timing of the main woodland fragmentation event by analysing: (1) the remaining levels of population genetic diversity and the relation to population size; (2) among‐population genetic differentiation; and (3) the difference in genetic diversity between the offspring and adult generation. We retrieved seven publications on the population genetics of five Polylepis spp. We did not find a relationship between population size and genetic diversity, and genetic differentiation was low compared with that reported for similar plant species. These findings do not support a history of long‐term fragmentation. The offspring showed a loss of genetic diversity and increasing differentiation compared with adults, suggesting that the main habitat fragmentation event is of relatively recent origin. For P. besseri, no significant differences were found between the adult and offspring genetic variation. We discuss the conservation and restoration consequences for this important high‐Andean genus. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 544–554.     

A millennial‐scale chronicle of evolutionary responses to cultural eutrophication in Daphnia

For an accurate assessment of the anthropogenic impacts on evolutionary change in natural populations, we need long‐term environmental, genetic and phenotypic data that predate human disturbances. Analysis of c. 1600 years of history chronicled in the sediments of South Center Lake, Minnesota, USA, revealed major environmental changes beginning c. 120 years ago coinciding with the initiation of industrialised agriculture in the catchment area. Population genetic structure, analysed using DNA from dormant eggs of the keystone aquatic herbivore, Daphnia pulicaria, suggested no change for c. 1500 years prior to striking shifts associated with anthropogenic environmental alterations. Furthermore, phenotypic assays on the oldest resurrected metazoan genotypes (potentially as old as c. 700 years) indicate significant shifts in phosphorus utilisation rates compared to younger genotypes. Younger genotypes show steeper reaction norms with high growth under high phosphorus (P), and low growth under low P, while ‘ancient’ genotypes show flat reaction norms, yet higher growth efficiency under low P. Using this resurrection ecology approach, environmental, genetic and phenotypic data spanning pre‐ and post‐industrialised agricultural eras clearly reveal the evolutionary consequences of anthropogenic environmental change.     

Population dynamics of a natural red deer population over 200 years detected via substantial changes of genetic variation

Most large mammals have constantly been exposed to anthropogenic influence over decades or even centuries. Because of their long generation times and lack of sampling material, inferences of past population genetic dynamics, including anthropogenic impacts, have only relied on the analysis of the structure of extant populations. Here, we investigate for the first time the change in the genetic constitution of a natural red deer population over two centuries, using up to 200‐year‐old antlers (30 generations) stored in trophy collections. To the best of our knowledge, this is the oldest DNA source ever used for microsatellite population genetic analyses. We demonstrate that government policy and hunting laws may have strong impacts on populations that can lead to unexpectedly rapid changes in the genetic constitution of a large mammal population. A high ancestral individual polymorphism seen in an outbreeding population (1813–1861) was strongly reduced in descendants (1923–1940) during the mid‐19th and early 20th century by genetic bottlenecks. Today (2011), individual polymorphism and variance among individuals is increasing in a constant‐sized (managed) population. Differentiation was high among periods (F_ST > ***); consequently, assignment tests assigned individuals to their own period with >85% probability. In contrast to the high variance observed at nuclear microsatellite loci, mtDNA (D‐loop) was monomorphic through time, suggesting that male immigration dominates the genetic evolution in this population.     

Hybridization effects and genetic diversity of the common and black‐tufted marmoset (Callithrix jacchus and Callithrix penicillata) mitochondrial control region

Hybridization is continually documented in primates, but effects of natural and anthropogenic hybridization on biodiversity are still unclear and differentiating between these contexts remains challenging in regards to primate evolution and conservation. Here, we examine hybridization effects on the mitochondrial DNA (mtDNA) control region of Callithrix marmosets, which provide a unique glimpse into interspecific mating under distinct anthropogenic and natural conditions. DNA was sampled from 40 marmosets along a 50‐km transect from a previously uncharacterized hybrid zone in NE Brazil between the ranges of Callithrix jacchus and Callithrix penicillata. DNA was also collected from 46 marmosets along a 30‐km transect in a hybrid zone in Rio de Janeiro state, Brazil, where exotic marmosets appeared in the 1980s. Combining Callithrix DNA sampled inside and outside of these hybrid zones, phylogenetic and network analyses show C. jacchus and C. penicillata being parental species to sampled hybrids. We expand limited Callithrix population genetics work by describing mtDNA diversity and demographic history of these parental species. We show ancient population expansion in C. jacchus and historically constant population size in C. penicillata, with the latter being more genetically diverse than the former. The natural hybrid zone contained higher genetic diversity relative to the anthropogenic zone. While our data suggest hybrid swarm formation within the anthropogenic zone due to removed physical reproductive barriers, this pattern is not seen in the natural hybrid zone. These results suggest different genetic dynamics within natural and anthropogenic hybridization contexts that carry important implications for primate evolution and conservation. Am J Phys Anthropol 155:522–536, 2014. © 2014 Wiley Periodicals, Inc.     

Gene flow and population structure of a solitary top carnivore in a human‐dominated landscape

While African leopard populations are considered to be continuous as demonstrated by their high genetic variation, the southernmost leopard population exists in the Eastern and Western Cape, South Africa, where anthropogenic activities may be affecting this population's structure. Little is known about the elusive, last free‐roaming top predator in the region and this study is the first to report on leopard population structuring using nuclear DNA. By analyzing 14 microsatellite markers from 40 leopard tissue samples, we aimed to understand the populations' structure, genetic distance, and gene flow (Nm). Our results, based on spatially explicit analysis with Bayesian methods, indicate that leopards in the region exist in a fragmented population structure with lower than expected genetic diversity. Three population groups were identified, between which low to moderate levels of gene flow were observed (Nm 0.5 to 3.6). One subpopulation exhibited low genetic differentiation, suggesting a continuous population structure, while the remaining two appear to be less connected, with low emigration and immigration between these populations. Therefore, genetic barriers are present between the subpopulations, and while leopards in the study region may function as a metapopulation, anthropogenic activities threaten to decrease habitat and movement further. Our results indicate that the leopard population may become isolated within a few generations and suggest that management actions should aim to increase habitat connectivity and reduce human–carnivore conflict. Understanding genetic diversity and connectivity of populations has important conservation implications that can highlight management of priority populations to reverse the effects of human‐caused extinctions.     

Spatial genetic analysis of two polyploid macrophytes reveals high connectivity in a modified wetland

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Molecular genetic analysis of Daphnia in the English Lake District: species identity, hybridisation and resting egg banks

• 1 Taxonomic issues in many Daphnia species complexes are often confused by a high degree of phenotypic plasticity and by interspecific hybridisation. Here, we employ molecular genetic tools to confirm the species composition and incidence of hybridisation in extant and resting egg populations of Daphnia from Windermere and Esthwaite Water in the English Lake District.
• 2 A combination of species‐diagnostic allozymes and mtDNA, confirms that contemporary populations are dominated by a single species, D. galeata.
• 3 We present the first account of genetic characterisation of dated ‘resting’ eggs using microsatellites and mtDNA, employing PCR‐based DNA recovery, thus providing a temporal dimension to taxonomic patterns. Thirty years ago, two species were present in Esthwaite, D. galeata and D. hyalina, but Windermere populations were dominated by D. galeata only.
• 4 The use of PCR‐based mtDNA RFLP analysis as a species‐diagnostic tool, and microsatellites to monitor clonal diversity, provide a valuable approach for long‐term studies, especially in populations free from the complicating effect of frequent hybridisation. The detailed limnological records available for many large lakes, and associated changes in land‐use, pollutants and climate, combined with long‐term ephippial molecular genetic data, provide opportunities for exploring natural and anthropogenic impacts on genetic and community structure.

     

Hybridization ddRAD‐sequencing for population genomics of nonmodel plants using highly degraded historical specimen DNA

Species’ responses at the genetic level are key to understanding the long‐term consequences of anthropogenic global change. Herbaria document such responses, and, with contemporary sampling, provide high‐resolution time‐series of plant evolutionary change. Characterizing genetic diversity is straightforward for model species with small genomes and a reference sequence. For nonmodel species—with small or large genomes—diversity is traditionally assessed using restriction‐enzyme‐based sequencing. However, age‐related DNA damage and fragmentation preclude the use of this approach for ancient herbarium DNA. Here, we combine reduced‐representation sequencing and hybridization‐capture to overcome this challenge and efficiently compare contemporary and historical specimens. Specifically, we describe how homemade DNA baits can be produced from reduced‐representation libraries of fresh samples, and used to efficiently enrich historical libraries for the same fraction of the genome to produce compatible sets of sequence data from both types of material. Applying this approach to both Arabidopsis thaliana and the nonmodel plant Cardamine bulbifera, we discovered polymorphisms de novo in an unbiased, reference‐free manner. We show that the recovered genetic variation recapitulates known genetic diversity in A. thaliana, and recovers geographical origin in both species and over time, independent of bait diversity. Hence, our method enables fast, cost‐efficient, large‐scale integration of contemporary and historical specimens for assessment of genome‐wide genetic trends over time, independent of genome size and presence of a reference genome.     

Unsustainable anthropogenic mortality disrupts natal dispersal and promotes inbreeding in leopards

Anthropogenic mortality of wildlife is typically inferred from measures of the absolute decline in population numbers. However, increasing evidence suggests that indirect demographic effects including changes to the age, sex, and social structure of populations, as well as the behavior of survivors, can profoundly impact population health and viability. Specifically, anthropogenic mortality of wildlife (especially when unsustainable) and fragmentation of the spatial distribution of individuals (home‐ranges) could disrupt natal dispersal mechanisms, with long‐term consequences to genetic structure, by compromising outbreeding behavior and gene flow. We investigate this threat in African leopards (Panthera pardus pardus), a polygynous felid with male‐biased natal dispersal. Using a combination of spatial (home‐range) and genetic (21 polymorphic microsatellites) data from 142 adult leopards, we contrast the structure of two South African populations with markedly different histories of anthropogenically linked mortality. Home‐range overlap, parentage assignment, and spatio‐genetic autocorrelation together show that historical exploitation of leopards in a recovering protected area has disrupted and reduced subadult male dispersal, thereby facilitating opportunistic male natal philopatry, with sons establishing territories closer to their mothers and sisters. The resultant kin‐clustering in males of this historically exploited population is comparable to that of females in a well‐protected reserve and has ultimately led to localized inbreeding. Our findings demonstrate novel evidence directly linking unsustainable anthropogenic mortality to inbreeding through disrupted dispersal in a large, solitary felid and expose the genetic consequences underlying this behavioral change. We therefore emphasize the importance of managing and mitigating the effects of unsustainable exploitation on local populations and increasing habitat fragmentation between contiguous protected areas by promoting in situ recovery and providing corridors of suitable habitat that maintain genetic connectivity.     

Living in two worlds: Evolutionary mechanisms act differently in the native and introduced ranges of an invasive plant

Identifying the factors that influence spatial genetic structure among populations can provide insights into the evolution of invasive plants. In this study, we used the common reed (Phragmites australis), a grass native in Europe and invading North America, to examine the relative importance of geographic, environmental (represented by climate here), and human effects on population genetic structure and its changes during invasion. We collected samples of P. australis from both the invaded North American and native European ranges and used molecular markers to investigate the population genetic structure within and between ranges. We used path analysis to identify the contributions of each of the three factors—geographic, environmental, and human‐related—to the formation of spatial genetic patterns. Genetic differentiation was observed between the introduced and native populations, and their genetic structure in the native and introduced ranges was different. There were strong effects of geography and environment on the genetic structure of populations in the native range, but the human‐related factors manifested through colonization of anthropogenic habitats in the introduced range counteracted the effects of environment. The between‐range genetic differences among populations were mainly explained by the heterogeneous environment between the ranges, with the coefficient 2.6 times higher for the environment than that explained by the geographic distance. Human activities were the primary contributor to the genetic structure of the introduced populations. The significant environmental divergence between ranges and the strong contribution of human activities to the genetic structure in the introduced range suggest that invasive populations of P. australis have evolved to adapt to a different climate and to human‐made habitats in North America.     

Human-mediated processes affecting distribution and genetic structure of Squalidus multimaculatus,a freshwater cyprinid with small spatial range

Endemic species typically have a narrow niche breadth, and are likely more vulnerable to extinction than more widespread taxa. Squalidus multimaculatus is a small cyprinid endemic to the Korean Peninsula, and its reported geographical range was restricted to several small rivers located along the southeast coast. Several populations of S. multimaculatus have supposedly been subject to a variety of recent anthropogenic actions. Here, we analyzed the pattern of genetic diversity within and among populations of S. multimaculatus using nine microsatellite loci to quantify the relative contributions of human-mediated processes to the contemporary distribution and genetic structure. Overall, low levels of genetic diversity were exhibited in the populations of S. multimaculatus. Genetic differentiations among populations were not completely represented by their geographical proximity, likely resulting from the low intrapopulation genetic variability and anthropogenic transplants. The most conspicuous outcome of the anthropogenic activities was the introgression of alleles from a closely related species, S. gracilis majimae. Our study showed that anthropogenic transplanting, even with only a small number of individuals, can challenge our conservation goal to maintain the species integrity that has long been shaped in evolutionary processes.     

Study of interactions between wild soybean subpopulations (<Emphasis Type="Italic">Glycine soja</Emphasis>) in the valley of the Tsukanovka river in the south of Russia’s Far East

Comparative analysis of the genetic structure of natural and anthropogenic populations of G. soja gives significant information about the formation of different populations and allows for the developing of measures for the preservation of the unique natural gene bank of wild soybean, which is a species closely related to cultivated soybean. In this study, ISSR-markers were used to carry out a comparative analysis of the genetic structure of natural and anthropogenic subpopulations of G. soja for studying the possible mutual influence of subpopulations of anthropogenic and natural phytocenosis on the formation of their genetic diversity and studying the genetic structure of natural subpopulations of wild soybean in the contact places between the two types of cenoses. As a result, the characteristics that describe the genetic diversity of the studied populations have been identified, and the important role of interaction between subpopulations of different phytocenoses in the formation of the spatial genetic structure of the population in the Tsukanovka river valley have been demonstrated.