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.     

Montane refugia predict population genetic structure in the Large‐blotched Ensatina salamander

Understanding the biotic consequences of Pleistocene range shifts and fragmentation remains a fundamental goal in historical biogeography and evolutionary biology. Here, we combine species distribution models (SDM) from the present and two late Quaternary time periods with multilocus genetic data (mitochondrial DNA and microsatellites) to evaluate the effect of climate‐induced habitat shifts on population genetic structure in the Large‐blotched Ensatina (Ensatina eschscholtzii klauberi), a plethodontid salamander endemic to middle and high‐elevation conifer forest in the Transverse and Peninsular Ranges of southern California and northern Baja California. A composite SDM representing the range through time predicts two disjunct refugia, one in southern California encompassing the core of the species range and the other in the Sierra San Pedro Mártir of northern Baja California at the southern limit of the species range. Based on our spatial model, we would expect a pattern of high connectivity among populations within the northern refugium and, conversely, a pattern of isolation due to long‐term persistence of the Sierra San Pedro Mártir population. Our genetic results are consistent with these predictions based on the hypothetical refugia in that (i) historical measures of population connectivity among stable areas are correlated with gene flow estimates; and (ii) there is strong geographical structure between separate refugia. These results provide evidence for the role of recent climatic change in shaping patterns of population persistence and connectivity within the Transverse and Peninsular Ranges, an evolutionary hotspot.     

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.     

Effective Population Size Dynamics and the Demographic Collapse of Bornean Orang-Utans

Bornean orang-utans experienced a major demographic decline and local extirpations during the Pleistocene and Holocene due to climate change, the arrival of modern humans, of farmers and recent commercially-driven habitat loss and fragmentation. The recent loss of habitat and its dramatic fragmentation has affected the patterns of genetic variability and differentiation among the remaining populations and increased the extinction risk of the most isolated ones. However, the contribution of recent demographic events to such genetic patterns is still not fully clear. Indeed, it can be difficult to separate the effects of recent anthropogenic fragmentation from the genetic signature of prehistoric demographic events. Here, we investigated the genetic structure and population size dynamics of orang-utans from different sites. Altogether 126 individuals were analyzed and a full-likelihood Bayesian approach was applied. All sites exhibited clear signals of population decline. Population structure is known to generate spurious bottleneck signals and we found that it does indeed contribute to the signals observed. However, population structure alone does not easily explain the observed patterns. The dating of the population decline varied across sites but was always within the 200–2000 years period. This suggests that in some sites at least, orang-utan populations were affected by demographic events that started before the recent anthropogenic effects that occurred in Borneo. These results do not mean that the recent forest exploitation did not leave its genetic mark on orang-utans but suggests that the genetic pool of orang-utans is also impacted by more ancient events. While we cannot identify the main cause for this decline, our results suggests that the decline may be related to the arrival of the first farmers or climatic events, and that more theoretical work is needed to understand how multiple demographic events impact the genome of species and how we can assess their relative contributions.     

Response of a southern temperate marsupial, the Tasmanian pademelon (Thylogale billardierii), to historical and contemporary forest fragmentation

Despite only limited Pleistocene glacial activity in the southern hemisphere, temperate forest species experienced complex distributional changes resulting from the combined effects of glaciation, sea level change and increased aridity. The effects of these historical processes on population genetic structure are now overlain by the effects of contemporary habitat modification. In this study, 10 microsatellites and 629 bp of the mitochondrial control region were used to assess the effects of historical forest fragmentation and recent anthropogenic habitat change on the broad-scale population genetic structuring of a southern temperate marsupial, the Tasmanian pademelon. A total of 200 individuals were sampled from seven sites across Tasmania and two islands in Bass Strait. High mitochondrial and nuclear genetic diversity indicated the maintenance of large historical population sizes. There was weak phylogeographical structuring of haplotypes, although all King Island haplotypes and three Tasmanian haplotypes formed a divergent clade implying the mid-Pleistocene isolation of a far northwestern population. Both the mitochondrial and nuclear data indicated a division of Tasmanian populations into eastern and western regions. This was consistent with a historical barrier resulting from increased aridity in the lowland 'midlands' region during glacial periods, and with a contemporary barrier resulting from recent habitat modification in that region. In Tasmania, gene flow appears to have been relatively unrestricted during glacial maxima in the west, while in the east there was evidence for historical expansion from at least one large glacial refuge and recolonization of Flinders Island.     

Spatiotemporally explicit demographic modelling supports a joint effect of historical barriers to dispersal and contemporary landscape composition on structuring genomic variation in a red‐listed grasshopper

Inferring the processes underlying spatial patterns of genomic variation is fundamental to understand how organisms interact with landscape heterogeneity and to identify the factors determining species distributional shifts. Here, we use genomic data (restriction site‐associated DNA sequencing) to test biologically informed models representing historical and contemporary demographic scenarios of population connectivity for the Iberian cross‐backed grasshopper Dociostaurus hispanicus, a species with a narrow distribution that currently forms highly fragmented populations. All models incorporated biological aspects of the focal taxon that could hypothetically impact its geographical patterns of genomic variation, including (a) spatial configuration of impassable barriers to dispersal defined by topographic landscapes not occupied by the species; (b) distributional shifts resulting from the interaction between the species bioclimatic envelope and Pleistocene glacial cycles; and (c) contemporary distribution of suitable habitats after extensive land clearing for agriculture. Spatiotemporally explicit simulations under different scenarios considering these aspects and statistical evaluation of competing models within an Approximate Bayesian Computation framework supported spatial configuration of topographic barriers to dispersal and human‐driven habitat fragmentation as the main factors explaining the geographical distribution of genomic variation in the species, with no apparent impact of hypothetical distributional shifts linked to Pleistocene climatic oscillations. Collectively, this study supports that both historical (i.e., topographic barriers) and contemporary (i.e., anthropogenic habitat fragmentation) aspects of landscape composition have shaped major axes of genomic variation in the studied species and emphasizes the potential of model‐based approaches to gain insights into the temporal scale at which different processes impact the demography of natural populations.     

Landscape effects on the contemporary genetic structure of Ruffed Grouse (Bonasa umbellus) populations

The amount of dispersal that occurs among populations can be limited by landscape heterogeneity, which is often due to both natural processes and anthropogenic activity leading to habitat loss or fragmentation. Understanding how populations are structured and mapping existing dispersal corridors among populations is imperative to both determining contemporary forces mediating population connectivity, and informing proper management of species with fragmented populations. Furthermore, the contemporary processes mediating gene flow across heterogeneous landscapes on a large scale are understudied, particularly with respect to widespread species. This study focuses on a widespread game bird, the Ruffed Grouse (Bonasa umbellus), for which we analyzed samples from the western extent of the range. Using three types of genetic markers, we uncovered multiple factors acting in concert that are responsible for mediating contemporary population connectivity in this species. Multiple genetically distinct groups were detected; microsatellite markers revealed six groups, and a mitochondrial marker revealed four. Many populations of Ruffed Grouse are genetically isolated, likely by macrogeographic barriers. Furthermore, the addition of landscape genetic methods not only corroborated genetic structure results, but also uncovered compelling evidence that dispersal resistance created by areas of unsuitable habitat is the most important factor mediating population connectivity among the sampled populations. This research has important implications for both our study species and other inhabitants of the early successional forest habitat preferred by Ruffed Grouse. Moreover, it adds to a growing body of evidence that isolation by resistance is more prevalent in shaping population structure of widespread species than previously thought.     

Urbanization reduces genetic connectivity in bobcats (Lynx rufus) at both intra– and interpopulation spatial scales

Urbanization is a major factor driving habitat fragmentation and connectivity loss in wildlife. However, the impacts of urbanization on connectivity can vary among species and even populations due to differences in local landscape characteristics, and our ability to detect these relationships may depend on the spatial scale at which they are measured. Bobcats (Lynx rufus) are relatively sensitive to urbanization and the status of bobcat populations is an important indicator of connectivity in urban coastal southern California. We genotyped 271 bobcats at 13,520 SNP loci to conduct a replicated landscape resistance analysis in five genetically distinct populations. We tested urban and natural factors potentially influencing individual connectivity in each population separately, as well as study–wide. Overall, landscape genomic effects were most frequently detected at the study–wide spatial scale, with urban land cover (measured as impervious surface) having negative effects and topographic roughness having positive effects on gene flow. The negative effect of urban land cover on connectivity was also evident when populations were analyzed separately despite varying substantially in spatial area and the proportion of urban development, confirming a pervasive impact of urbanization largely independent of spatial scale. The effect of urban development was strongest in one population where stream habitat had been lost to development, suggesting that riparian corridors may help mitigate reduced connectivity in urbanizing areas. Our results demonstrate the importance of replicating landscape genetic analyses across populations and considering how landscape genetic effects may vary with spatial scale and local landscape structure.     

Colonization from divergent ancestors: glaciation signatures on contemporary patterns of genomic variation in Collared Pikas (Ochotona collaris)

Identifying the genetic structure of a species and the factors that drive it is an important first step in modern population management, in part because populations evolving from separate ancestral sources may possess potentially different characteristics. This is especially true for climate‐sensitive species such as pikas, where the delimitation of distinct genetic units and the characterization of population responses to contemporary and historical environmental pressures are of particular interest. We combined a restriction site‐associated DNA sequencing (RADSeq) data set containing 4156 single nucleotide polymorphisms with ecological niche models (ENMs) of present and past habitat suitability to characterize population composition and evaluate the effects of historical range shifts, contemporary climates and landscape factors on gene flow in Collared Pikas, which are found in Alaska and adjacent regions of northwestern Canada and are the lesser‐studied of North America's two pika species. The results suggest that contemporary environmental factors contribute little to current population connectivity. Instead, genetic diversity is strongly shaped by the presence of three ancestral lineages isolated during the Pleistocene (~148 and 52 kya). Based on ENMs and genetic data, populations originating from a northern refugium experienced longer‐term stability, whereas both southern lineages underwent population expansion – contradicting the southern stability and northern expansion patterns seen in many other taxa. Current populations are comparable with respect to generally low diversity within populations and little‐to‐no recent admixture. The predominance of divergent histories structuring populations implies that if we are to understand and manage pika populations, we must specifically assess and accurately account for the forces underlying genetic similarity.     

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.     

Genetic assessment of lake sturgeon (<Emphasis Type="Italic">Acipenser fulvescens</Emphasis>) population structure in the Ottawa River

Lake sturgeon (Acipenser fulvescens) are of conservation concern throughout their range. Many populations are dependent on fluvial habitats which have been increasingly impacted and fragmented by dams and human development. Although lake sturgeon were once abundant in the Ottawa River and its tributaries, historical commercial harvests and other anthropogenic factors caused severe declines and low contemporary numbers in lake sturgeon populations. Contemporary habitat fragmentation by dams may be increasing isolation among habitat patches and local rates of decline, raising concerns for persistence of local populations. We used microsatellite DNA markers to assess population structure and diversity of lake sturgeon in the Ottawa River, and analyzed samples from 10 sites that represent more than 500 km of riverine habitat. To test for evidence of anthropogenic fragmentation, patterns of genetic diversity and connectivity within and among river segments were tested for concordance with geographic location, separation by distance and obstacles to migration, considering both natural and artificial barriers as well as barrier age. Despite extensive habitat fragmentation throughout the Ottawa River, statistical analyses failed to refute panmixia of lake sturgeon in this system. Although the long generation time of lake sturgeon appears to have effectively guarded against the negative genetic impacts of habitat fragmentation and loss so far, evidence from demographic studies indicates that restoring connectivity among habitats is needed for the long-term conservation and management of this species throughout this river system.     

Genetic signature of population fragmentation varies with mobility in seven bird species of a fragmented Kenyan cloud forest

Habitat fragmentation can restrict geneflow, reduce neighbourhood effective population size, and increase genetic drift and inbreeding in small, isolated habitat remnants. The extent to which habitat fragmentation leads to population fragmentation, however, differs among landscapes and taxa. Commonly, researchers use information on the current status of a species to predict population effects of habitat fragmentation. Such methods, however, do not convey information on species-specific responses to fragmentation. Here, we compare levels of past population differentiation, estimated from microsatellite genotypes, with contemporary dispersal rates, estimated from multi-strata capture-recapture models, to infer changes in mobility over time in seven sympatric, forest-dependent bird species of a Kenyan cloud forest archipelago. Overall, populations of sedentary species were more strongly differentiated and clustered compared to those of vagile ones, while geographical patterning suggested an important role of landscape structure in shaping genetic variation. However, five of seven species with broadly similar levels of genetic differentiation nevertheless differed substantially in their current dispersal rates. We conclude that post-fragmentation levels of vagility, without reference to past population connectivity, may not be the best predictor of how forest fragmentation affects the life history of forest-dependent species. As effective conservation strategies often hinge on accurate prediction of shifts in ecological and genetic relationships among populations, conservation practices based solely upon current population abundances or movements may, in the long term, prove to be inadequate.     

Waterscape genetics of the yellow perch ( Perca flavescens): patterns across large connected ecosystems and isolated relict populations

Comparisons of a species' genetic diversity and divergence patterns across large connected populations vs. isolated relict areas provide important data for understanding potential response to global warming, habitat alterations and other perturbations. Aquatic taxa offer ideal case studies for interpreting these patterns, because their dispersal and gene flow often are constrained through narrow connectivity channels that have changed over geological time and/or from contemporary anthropogenic perturbations. Our research objective is to better understand the interplay between historic influences and modern‐day factors (fishery exploitation, stocking supplementation and habitat loss) in shaping population genetic patterns of the yellow perch Perca flavescens (Percidae: Teleostei) across its native North American range. We employ a modified landscape genetics approach, analysing sequences from the entire mitochondrial DNA control region and 15 nuclear DNA microsatellite loci of 664 spawning adults from 24 populations. Results support that perch from primary glacial refugium areas (Missourian, Mississippian and Atlantic) founded contemporary northern populations. Genetic diversity today is highest in southern (never glaciated) populations and also is appreciable in northern areas that were founded from multiple refugia. Divergence is greater among isolated populations, both north and south; the southern Gulf Coast relict populations are the most divergent, reflecting their long history of isolation. Understanding the influence of past and current waterway connections on the genetic structure of yellow perch populations may help us to assess the roles of ongoing climate change and habitat disruptions towards conserving aquatic biodiversity.     

When recent and evolutionary histories meet: deciphering temporal events from contemporary patterns of mtDNA from fishers (Martes pennanti) in north‐eastern North America

The current spatial distribution of genetic lineages across a region should reflect the complex interplay of both historical and contemporary processes. Postglacial expansion and recolonization in the distant past, in combination with more recent events with anthropogenic effects such as habitat fragmentation and overexploitation, can help shape the pattern of genetic structure observed in contemporary populations. In this study, we characterize the spatial distribution of mtDNA lineages for fisher (Martes pennanti) in north‐eastern North America. The history of fishers in this region is well understood and thus provides an opportunity to interpret patterns of genetic structure in the light of known historical (e.g. recolonization from glacial refugia) and contemporary events (e.g. reintroductions, fragmentation and natural recolonization). Our results indicate that fishers likely recolonized north‐eastern North America from a single Pleistocene refugium. Three genetically distinct remnant populations persisted through the population declines of the 1800s and served as sources for multiple reintroductions and natural recolonizations that have restored the fisher throughout north‐eastern North America. However, the spatial genetic structure of genetic lineages across the region still reflects the three remnant populations.     

Spatial differences in genetic diversity and northward migration suggest genetic erosion along the boreal caribou southern range limit and continued range retraction

With increasing human activities and associated landscape changes, distributions of terrestrial mammals become fragmented. These changes in distribution are often associated with reduced population sizes and loss of genetic connectivity and diversity (i.e., genetic erosion) which may further diminish a species' ability to respond to changing environmental conditions and lead to local population extinctions. We studied threatened boreal caribou (Rangifer tarandus caribou) populations across their distribution in Ontario/Manitoba (Canada) to assess changes in genetic diversity and connectivity in areas of high and low anthropogenic activity. Using data from >1,000 caribou and nine microsatellite loci, we assessed population genetic structure, genetic diversity, and recent migration rates using a combination of network and population genetic analyses. We used Bayesian clustering analyses to identify population genetic structure and explored spatial and temporal variation in those patterns by assembling networks based on R_ST and F_ST as historical and contemporary genetic edge distances, respectively. The Bayesian clustering analyses identified broad‐scale patterns of genetic structure and closely aligned with the R_ST network. The F_ST network revealed substantial contemporary genetic differentiation, particularly in areas presenting contemporary anthropogenic disturbances and habitat fragmentation. In general, relatively lower genetic diversity and greater genetic differentiation were detected along the southern range limit, differing from areas in the northern parts of the distribution. Moreover, estimation of migration rates suggested a northward movement of animals away from the southern range limit. The patterns of genetic erosion revealed in our study suggest ongoing range retraction of boreal caribou in central Canada.     

Restoration of Fragmented Landscapes for the Conservation of Birds: A General Framework and Specific Recommendations for Urbanizing Landscapes

Humans fragment landscapes to the detriment of wildlife. We review why fragmentation is detrimental to wildlife (especially birds), review the effects of urbanization on birds inhabiting nearby native habitats, suggest how restoration ecologists can minimize these effects, and discuss future research needs. We emphasize the importance of individual fitness to determining community composition. This means that reproduction, survivorship, and dispersal (not simply community composition) must be maintained, restored, and monitored. We suggest that the severity of the effects of fragmentation are determined by (1) the natural disturbance regime, (2) the similarity of the anthropogenic matrix to the natural matrix, and (3) the persistence of the anthropogenic change. As a result, urbanization is likely to produce greater effects of fragmentation than either agriculture or timber harvest. Restoration ecologists, land managers, and urban planners can help maintain native birds in fragmented landscapes by a combination of short‐ and long‐term actions designed to restore ecological function (not just shape and structure) to fragments, including: (1) maintaining native vegetation, deadwood, and other nesting structures in the fragment, (2) managing the landscape surrounding the fragment (matrix), not just the fragment, (3) making the matrix more like the native habitat fragments, (4) increasing the foliage height diversity within fragments, (5) designing buffers that reduce penetration of undesirable agents from the matrix, (6) recognizing that human activity is not compatible with interior conditions, (7) actively managing mammal populations in fragments, (8) discouraging open lawn on public and private property, (9) providing statutory recognition of the value of complexes of small wetlands, (10) integrating urban parks into the native habitat system, (11) anticipating urbanization and seeking creative ways to increase native habitat and manage it collectively, (12) reducing the growing effects of urbanization on once remote natural areas, (13) realizing that fragments may be best suited to conserve only a few species, (14) developing monitoring programs that measure fitness, and (15) developing a new educational paradigm.     

Spatial and temporal patterns of genetic diversity in an endangered Hawaiian honeycreeper,the Hawaii Akepa (<Emphasis Type="Italic">Loxops coccineus coccineus</Emphasis>)

As a result of disease, habitat destruction, and other anthropogenic factors, the Hawaii Akepa (Loxops coccineus coccineus) currently occupies <10% of its original range and exists in five disjunct populations, raising concerns about what effect such reduction and fragmentation has had on the connectivity and diversity of Akepa populations. In this study, we used both historical and contemporary samples to assess genetic diversity and structure in this endangered Hawaiian honeycreeper. We generated sequence data from two mtDNA regions (ND2, control region) and two nuclear introns for contemporary samples representing three of the five current populations. We also generated control region sequence data for museum specimens collected over 100 years ago from throughout the historical range of the bird. Results indicate that despite recent declines and fragmentation, genetic diversity has not been lost. We detected a modest level of genetic differentiation, which followed a combined pattern of isolation-by-barriers and isolation-by-distance, across the historical range of Akepa. The similarly low level of differentiation observed between the contemporary populations indicates that not much divergence, if any, has occurred post-fragmentation. Rather, the present structure seen likely reflects the historical pattern of distribution. 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_e, though crude, suggest Hawaii Akepa were at least an order of magnitude more abundant prior to the decline.     

After 100 years: hydroelectric dam-induced life-history divergence and population genetic changes in sockeye salmon (<Emphasis Type="Italic">Oncorhynchus nerka</Emphasis>)

Understanding the impact of barriers and habitat fragmentation on the ecology and genetics of species is of broad interest to many biologists. In aquatic systems, hydroelectric dams often present an impenetrable barrier to migratory fish and can have negative effects on their persistence. Hydroelectric dams constructed in the Coquitlam and Alouette Rivers in the Fraser River drainage (British Columbia, Canada) in the early 1900s were thought to have led to complete loss of anadromous sockeye salmon from both rivers. For both reservoirs, recent water release programs resulted in the unexpected downstream migration of juvenile sockeye salmon and the subsequent upstream migration of adults towards the reservoir 2 years later. Here we investigate the evolutionary impact of dams on the sockeye salmon migration behavior by investigating the genetic distinction between migratory and non-migratory individuals within the Alouette and Coquitlam reservoirs. We also compare historical and contemporary genetic connectivity among 11 Lower Fraser River sockeye sites to infer recent population connectivity changes that might have been influenced by anthropogenic activities. Our molecular genetic analyses show a genetic distinction between the sea-run and resident individuals from the Coquitlam reservoir and population splitting time estimates suggest a very recent divergence between them. These results indicate a genetic component to migration behavior. For our broader survey from 11 sites, our comparisons suggest a general decline in gene flow, with a few interesting exceptions. In summary, our results suggest (i) early stage divergence between life history forms of sockeye salmon within one reservoir, and (ii) recent changes in genetic connectivity among Lower Fraser River populations; both of these results have potential recovery implications for historically migratory populations that were affected by anthropogenic barriers such as hydroelectric dams.     

Phylogeography of Pseudacris regilla (Anura: Hylidae) in western North America, with a proposal for a new taxonomic rearrangement

The Baja California populations of Pseudacris regilla, a widespread species in Western North America ranging from British Columbia to southern Baja California, are characterized by extensive geographic fragmentation. We performed phylogeographic and historical demographic analyses on 609 bp of the cytochrome b mitochondrial gene of 110 individuals representing 28 populations to determine the relative influences of current and historical processes in shaping the present distribution of genetic diversity on the Baja California Peninsula. Haplotypes from this area were nested in a clade with three well-differentiated groups. Two of these groups are from Baja California Sur and another is from California and Baja California. The estimated date for the split of these groups, between 0.9-1 Ma, fits with previously proposed hypotheses of vicariance due to different transpeninsular seaways, although successive population fragmentation and expansion due to climatic oscillations during Pleistocene glaciations cannot be discarded. Historical demographic analyses detected signs of past population expansions, especially in the southernmost group. With respect to populations north of this region, two older clades were identified, one with haplotypes mainly distributed in central California, and the other corresponding to the northern half of the species range, in what apparently is a recurrent pattern in the Pacific coast of North America. Based on the concordance between mt-DNA and available allozyme data indicating that these species have a long independent evolutionary history, we propose to consider the three major clades as distinct species: P. regilla, P. pacifica, and P. hypochondriaca.     

Range-wide fragmentation in a threatened fish associated with post-European settlement modification in the Murray–Darling Basin,Australia

Distinguishing the relative influence of historic (i.e. natural) versus anthropogenic factors in metapopulation structure is an important but often overlooked step in management programs of threatened species. Biotas in freshwater wetlands and floodplains, such as those in the Murray–Darling Basin (MDB)—one of Australia’s most impacted ecosystems, are particularly susceptible to anthropogenic fragmentation. Here we present a comprehensive multilocus assessment of genetic variation in the threatened southern pygmy perch Nannoperca australis (578 individuals; 45 localities; microsatellite, allozyme and mitochondrial DNA datasets), an ecological specialist with low dispersal potential. We assess patterns of spatial structure and genetic diversity in populations spanning the highly fragmented MDB and test whether recent anthropogenic modification has disrupted range-wide connectivity. We detected strong and hierarchical population structure, very low genetic diversity and lack of contemporary gene flow across the MDB. In contrast, the apparent absence of pronounced or long-term phylogeographic structure suggests that observed population divergences generally do not reflect deeply historic natural fragmentation. Coalescent-based analyses supported this inference, revealing that divergence times between populations from the upper and lower MDB fall into the period of European settlement. It appears that the observed contemporary isolation of populations is partly explained by the severe modification of the MDB post-dating the onset of European settlement. Our integrated approach substantially improves the interpretation of how fragmentation impacts present-day biodiversity. It also provides novel contributions for risk-assessing management actions in the context of captive breeding and translocations of small freshwater fishes, a group of increasing global conservation concern.