Estimating divergence time for two evolutionarily significant units of a protected fish species

The evolutionarily significant unit concept provides a powerful tool for conserving biodiversity below the species level, but temporal criteria are often used explicitly or implicitly in the operational definitions of evolutionarily significant units (ESUs). Such temporal considerations have important implications for recently diverged taxa, as is the case with the White sands pupfish (Cyprinodon tularosa). This species consists of two native populations previously designated as the Malpais Spring and Salt Creek ESUs based on allele frequency differences at nuclear markers and their ecologically divergent habitats; despite a lack of reciprocal monophyly. Isolation of these two ESUs presumably occurred during the mid-Holocene, but an alternative hypothesis is that the populations were isolated due to changes in surface hydrology associated with overgrazing in the late 19th and early 20th centuries. We assayed 13 microsatellite loci and applied an Approximate Bayesian Computation analysis to estimate time of divergence between the two populations. Our reference table consisted of 1,000,000 simulated data sets, and we used three different models, each having different combinations of summary statistics. Estimates of median divergence time varied from approximately 6,500–11,000 generations (3,250–11,000 years). These findings support the hypothesis that Malpais Spring and Salt Creek having been isolated for a least a few millennia, and together with previously documented adaptive divergence, argues for continued management as separate conservation units. We consider the temporal constraints for defining evolutionary significance as it relates to recently diverged populations occupying ecologically divergent habitats.     

Effects of habitat fragmentation and soil quality on reproduction in two heathland Genista species

Habitat fragmentation decreases plant population size and increases population isolation, as well as altering patterns of plant–animal interactions, all of which may reduce plant fitness. Here, we studied effects of habitat fragmentation (in terms of population size and isolation) and soil quality on the reproduction of two rare legume species, Genista anglica (13 populations) and Genista pilosa (14 populations), confined to remnants of acidic and nutrient‐poor Calluna heathlands. Single individuals of the Genista plants are impossible to distinguish; population size was therefore estimated according to the area occupied (referred to as population size hereafter). We collected soil samples in all heathland sites to determine content of soil water, C, N, P, Ca, K and Mg. In both species values of soil pH and C/N ratio, as well as content of soil P and base cations, reflected the highly acidic and nutrient‐poor environment of the heathlands. Population sizes were unrelated to soil quality. Although the two Genista species are similar in morphology and ecology, effects of explanatory variables on reproduction were largely inconsistent across species. In G. anglica, population size had a positive impact on all reproductive variables except germination rate, which, in contrast, was the only variable affected positively by population size in G. pilosa. In both species, mean total reproductive output, calculated as the product of total seed mass per shoot and total germination, increased with increasing water content and decreased with increasing P. In G. anglica, we found positive effects of the C/N ratio on all reproductive variables except mean single and total seed mass per shoot. In summary, in both species reproductive success per shoot decreased with increasing soil nutrient availability in the heathland sites. The infestation of two large populations of G. pilosa with the pre‐dispersal, seed‐predating weevil Apion compactum had no significant effect on reproduction of the populations.     

Genetic and ecological consequences of recent habitat fragmentation in a narrow endemic plant species within an urban context

Understanding the timescales that shape spatial genetic structure is pivotal to ascertain the impact of habitat fragmentation on the genetic diversity and reproductive viability of long-lived plant populations. Combining genetic and ecological information with current and past fragmentation conditions allows the identification of the main drivers important in shaping population structure and declines in reproduction, which is crucial for informing conservation strategies. Using historic aerial photographs, we defined the past fragmentation conditions for the shrub Conospermum undulatum, a species now completely embedded in an urban area. We explored the impact of current and past conditions on its genetic layout and assessed the effects of genetic and environmental factors on its reproduction. The historically high structural connectivity was evident in the genetics of the species. Despite the current intense fragmentation, we found similar levels of genetic diversity across populations and a weak spatial genetic structure. Historical connectivity was negatively associated with genetic differentiation among populations and positively related to within-population genetic diversity. Variation partitioning of reproductive performance explained?~?66% of the variance, showing significant influences for genetic (9%), environmental (15%), and combined (42%) fractions. Our study highlights the importance of considering the historical habitat dynamics when investigating fragmentation consequences in long-lived plants. A detailed characterization of fragmentation from 1953 has shown how low levels of genetic fixation are due to extensive gene flow through the non-fragmented landscape. Moreover, knowledge of the relationships between genetic and environmental variation and reproduction can help to implement effective conservation strategies, particularly in highly dynamic landscapes.

     

Experimental habitat fragmentation and invertebrate grazing in a herbaceous grassland species

A field experiment was conducted to examine the effects of habitat fragmentation on herbivore damage to individually tagged leaves of Betonica officinalis rosettes. Fragments of different size and corresponding control plots were established at three study sites in nutrient-poor calcareous grasslands in the northern Swiss Jura mountains. Leaf damage was recorded three times over the growing season (late spring, summer and early autumn). Five years after the initiation of the fragmentation, the density of rosettes did not differ between fragments and control plots. The number of leaves per rosette was higher in fragments than in control plots in summer but not in late spring and early autumn. The extent of leaf damage, expressed as proportion of leaf area removed by invertebrate herbivores, increased over the vegetation period. Leaf damage was greater in fragments than in control plots at two study sites, whereas the opposite (less strongly expressed) was found at the third site. Number of species and density (individuals per m²) of potential herbivores (gastropods and grasshoppers) were recorded in all fragments and control plots. Effects of fragmentation on the number of species and densities depended on plot size and differed between gastropods and grasshoppers. Leaf damage in fragments increased with increasing density of gastropods if the third site, which had lowest leaf damage, was excluded. Such a positive relationship was neither found in control plots nor for grasshopper densities. Thus, movement of gastropods in fragments was probably restricted which resulted in increased feeding pressure at least in two sites. However, even if our fragmentation experiment was well designed and replicated, the interpretation of these experimental results remains difficult because there was large site-to-site and seasonal variation.     

Characterizing the movements and habitat use of two fish species of concern in a regulated ecosystem

Hydrobiologia - In freshwater ecosystems in the northwest United States, the distribution and movements of fish between their essential habitats are particularly impacted by the presence of...     

Parasite phylogeographical congruence with salmon host evolutionarily significant units: implications for salmon conservation

Comparative phylogeographical studies between parasites and their hosts or with biogeographical regions are useful to predict parasite dispersal potential over a broad geographical range. We used both microsatellite markers and mtDNA sequence data from a trematode parasite, Plagioporus shawi, to test for congruence across two evolutionarily significant unit (ESU) boundaries of its salmonid hosts (Oncorhynchus spp.). We find congruent patterns with the nuclear loci of P. shawi and the ESU boundaries of its salmonid hosts. This pattern indicates that broad-scale phylogeographical patterns of a parasite can be predicted by the biogeographical history of their hosts. Furthermore, this pattern provides independent support for these ESU boundaries as biologically relevant barriers. The mtDNA shows some discordance with nuclear loci and a level of genetic differentiation greater than can be explained by genetic drift. Thus, the mtDNA cannot be used in isolation to infer the population history of P. shawi. The genetic differentiation at both the nuclear and mtDNA markers will be useful for salmon fisheries management by providing a tool to assign ocean-migrating salmonids back to their freshwater population of origin.     

The Meeting of Waters, a possible shelter of evolutionary significant units for Amazonian fish

Identification of priority conservation areas is crucial for safeguarding freshwater ecosystems. Occurrence of unique populations and/or evolutionary significant units for key species is one of the most frequent reasons for protecting a region or location. In this study we have studied two of the most important fisheries resources of the Amazon basin, Curimata and Tambaqui, from different areas, in order to identify common zones of special diversity. Employing the Barcoding cytochrome oxidase I gene as a genetic tool, we have detected a clear differentiation of the populations inhabiting the Meeting of Waters and the rest of the basin for both species. This area corresponds to the confluence of the Solimões and the Negro rivers, of different physicochemical water characteristics, at the Brazilian city of Manaus in central Amazonas. The Meeting of Waters area (near Manaus) could be recommended as a potential area subject of special management, given its apparent role as a shelter for evolutionary significant units.     

Inferring evolutionarily significant units of bacterial diversity from broad environmental surveys of single-locus data

By far the greatest challenge for diversity studies is to characterize the diversity of prokaryotes, which probably encompasses billions of species, most of which are unculturable. Recent advances in theory and analysis have focused on multi-locus approaches and on combined analysis of molecular and ecological data. However, broad environmental surveys of bacterial diversity still rely on single-locus data, notably 16S ribosomal DNA, and little other detailed information. Evolutionary methods of delimiting species from single-locus data alone need to consider population genetic and macroevolutionary theories for the expected levels of interspecific and intraspecific variation. We discuss the use of a recent evolutionary method, based on the theory of coalescence within independently evolving populations, compared with a traditional approach that uses a fixed threshold divergence to delimit species.     

Cryptic differences in dispersal lead to differential sensitivity to habitat fragmentation in two bumblebee species

Habitat loss has led to fragmentation of populations of many invertebrates, but social hymenopterans may be particularly sensitive to habitat fragmentation due to their low effective population sizes. The impacts of fragmentation depend strongly on dispersal abilities, but these are difficult to quantify. Here, we quantify and compare dispersal abilities of two bumblebee species, Bombus muscorum and Bombus jonellus , in a model island system. We use microsatellites to investigate population genetic structuring, dispersal and spatial patterns in genetic diversity. Populations of both species showed significant structuring, and isolation by distance, but this was markedly greater in B. muscorum (θ = 0.13) than in B. jonellus (θ = 0.034). This difference could reflect a higher effective population size in B. jonellus compared to B. muscorum , but this is not consistent with the observed abundance of the two species. We argue that it is more likely that B. jonellus has a higher propensity to disperse than B. muscorum . This will influence their relative susceptibility to habitat fragmentation and may in part explain differential declines of mainland populations of these and other bumblebee species.     

Differential threshold effects of habitat fragmentation on gene flow in two widespread species of bush crickets

Effects of habitat fragmentation on genetic diversity vary among species. This may be attributed to the interacting effects of species traits and landscape structure. While widely distributed and abundant species are often considered less susceptible to fragmentation, this may be different if they are small sized and show limited dispersal. Under intensive land use, habitat fragmentation may reach thresholds at which gene flow among populations of small-sized and dispersal-limited species becomes disrupted. Here, we studied the genetic diversity of two abundant and widespread bush crickets along a gradient of habitat fragmentation in an agricultural landscape. We applied traditional (G(ST), θ) and recently developed (G'ST', D) estimators of genetic differentiation on microsatellite data from each of twelve populations of the grassland species Metrioptera roeselii and the forest-edge species Pholidoptera griseoaptera to identify thresholds of habitat fragmentation below which genetic population structure is affected. Whereas the grassland species exhibited a uniform genetic structuring (G(ST) = 0.020-0.033; D = 0.085-0.149) along the whole fragmentation gradient, the forest-edge species' genetic differentiation increased significantly from D < 0.063 (G(ST) < 0.018) to D = 0.166 (G(ST) = 0.074), once the amount of suitable habitat dropped below a threshold of 20% and its proximity decreased substantially at the landscape scale. The influence of fragmentation on genetic differentiation was qualitatively unaffected by the choice of estimators of genetic differentiation but quantitatively underestimated by the traditional estimators. These results indicate that even for widespread species in modern agricultural landscapes fragmentation thresholds exist at which gene flow among suitable habitat patches becomes restricted.     

Correction to: Genetic and ecological consequences of recent habitat fragmentation in a narrow endemic plant species within an urban context

Biodiversity and Conservation -     

Effects of habitat fragmentation on the fitness of two common wetland species,Carex davalliana and Succisa pratensis

Small habitat size and spatial isolation may cause plant populations to suffer from genetic drift and inbreeding, leading to a reduced fitness of individual plants. We examined the germination, establishment, growth, and reproductive capacity of two characteristic species of mown fen meadows, Carex davalliana, and Succisa pratensis, common in Switzerland. Plants were grown from seeds, which were collected in 18 habitat islands, differing in size and in degree of isolation. We used both common garden and reciprocal transplant experiments to assess effects of habitat fragmentation. In the common garden, plants of Carex originating from small habitat islands yielded 35% less biomass, 30% fewer tillers, and 45% fewer flowering tillers than plants from larger ones. In contrast, plants of Succisa originating from small habitat islands yielded 19% more biomass, 14% more flower heads and 35% more flowers per flower head than plants from larger ones. Moreover, plants of Succisa from small isolated habitats yielded 32% more rosettes than did plants from small connected islands. Reciprocally transplanted plants of Succisa originating from small habitat islands produced 7% more rosettes than plants from larger ones. There was no effect of small habitat size and isolation on germination and establishment of both species in the field. Our results document genetic differences in performance attributable to habitat fragmentation in both species. We suggest that fitness loss in Carex is caused by inbreeding depression, whereas in Succisa the differences in fitness are more likely caused by genetic differentiation. Our study implies that habitat fragmentation affects common habitat-specific species, such as Carex and Succisa, as well as rare ones.     

Genetic variability and the effect of habitat fragmentation in spotted suslik Spermophilus suslicus populations from two different regions

Endangered species worldwide exist in remnant populations, often within fragmented landscapes. Although assessment of genetic diversity in fragmented habitats is very important for conservation purposes, it is usually impossible to evaluate the amount of diversity that has actually been lost. Here, we compared population structure and levels of genetic diversity within populations of spotted suslik Spermophilus suslicus, inhabiting two different parts of the species range characterized by different levels of habitat connectivity. We used microsatellites to analyze 10 critically endangered populations located at the western part of the range, where suslik habitat have been severely devastated due to agriculture industrialization. Their genetic composition was compared with four populations from the eastern part of the range where the species still occupies habitat with reasonable levels of connectivity. In the western region, we detected extreme population structure (F _ST = 0.20) and levels of genetic diversity (Allelic richness ranged from 1.45 to 3.07) characteristic for highly endangered populations. Alternatively, in the eastern region we found significantly higher allelic richness (from 5.09 to 5.81) and insignificant population structure (F _ST = 0.03). As we identified a strong correlation between genetic and geographic distance and a lack of private alleles in the western region, we conclude that extreme population structure and lower genetic diversity is due to recent habitat loss. Results from this study provide guidelines for conservation and management of this highly endangered species.     

Population size,habitat fragmentation,and the nature of adaptive variation in a stream fish

Whether and how habitat fragmentation and population size jointly affect adaptive genetic variation and adaptive population differentiation are largely unexplored. Owing to pronounced genetic drift, small, fragmented populations are thought to exhibit reduced adaptive genetic variation relative to large populations. Yet fragmentation is known to increase variability within and among habitats as population size decreases. Such variability might instead favour the maintenance of adaptive polymorphisms and/or generate more variability in adaptive differentiation at smaller population size. We investigated these alternative hypotheses by analysing coding-gene, single-nucleotide polymorphisms associated with different biological functions in fragmented brook trout populations of variable sizes. Putative adaptive differentiation was greater between small and large populations or among small populations than among large populations. These trends were stronger for genetic population size measures than demographic ones and were present despite pronounced drift in small populations. Our results suggest that fragmentation affects natural selection and that the changes elicited in the adaptive genetic composition and differentiation of fragmented populations vary with population size. By generating more variable evolutionary responses, the alteration of selective pressures during habitat fragmentation may affect future population persistence independently of, and perhaps long before, the effects of demographic and genetic stochasticity are manifest.     

Genetic structure,diversity and distribution of a threatened lizard affected by widespread habitat fragmentation

Understanding the demographic consequences of habitat loss on populations is essential for the conservation of threatened species. The threatened swamp skink (Lissolepis coventryi) is restricted to fragmented wetland habitats in Victoria and southeast South Australia. It has experienced significant habitat loss in the last 150 years, particularly around the Melbourne metropolitan area, where several small and isolated populations remain. Using mtDNA and nuDNA SNPs, we examined distribution patterns and population structure to infer evolutionary history and genetic distinctiveness of populations throughout the species’ range. For populations in the Melbourne metropolitan area, we examined genetic diversity. We found the species to be highly divergent, separating into two distinct lineages to the east and west of Melbourne, likely due to geological and climate influences causing isolation of populations. Species’ detectability was low, particularly in the far east despite relatively intact habitat and presumed higher abundance. Melbourne populations showed signs of limited genetic diversity. We suggest that translocations to promote gene diversity amongst these populations, together with habitat restoration and protection, present an important management strategy for L. coventryi.

     

Mangroves as a habitat for fish and prawns

Mangrove inlets and creeks in Selangor, Malaysia are the habitat for 119 species of fish and 9 species of prawns. The majority of fish and all prawns sampled in the inlets were juveniles. The common fish species in the inlets in terms of weight wereArius sagor, Ambassis gymnocephalus, Liza subviridis, Toxotes jaculator, Sphyraena barracuda andLates calcarifer. Prawns were represented by juvenilePenaeus penicillatus, P. merguiensis, P. indicus, Metapenaeus brevicornis andM. affinis. Samples from enclosure traps set on mudflats during ebbing water captured 37 species of fish and 11 species of prawns. The role of mangroves as nursery and feeding grounds for fish and prawns is reviewed in the light of recent work in Selangor. It is apparent that mangroves support fisheries by providing habitat and food.     

Genetic diversity and population structure of a protected species: Polygala tenuifolia Willd

Polygala tenuifolia Willd. is an important protected species used in traditional Chinese medicine. In the present study, amplified fragment length polymorphism (AFLP) markers were employed to characterize the genetic diversity in wild and cultivated P. tenuifolia populations. Twelve primer combinations of AFLP produced 310 unambiguous and repetitious bands. Among these bands, 261 (84.2%) were polymorphic. The genetic diversity was high at the species level: percentage of polymorphic loci (PPL) = 84.2%, Nei's gene diversity (h) = 0.3296 and Shannon's information index (I) = 0.4822. Between the two populations, the genetic differentiation of 0.1250 was low and the gene flow was relatively high, at 3.4989. The wild population (PPL = 81.9%, h = 0.3154, I = 0.4635) showed a higher genetic diversity level than the cultivated population (PPL = 63.9%, h = 0.2507, I = 0.3688). The results suggest that the major factors threatening the persistence of P. tenuifolia resources are ecological and human factors rather than genetic. These results will assist with the design of conservation and management programs, such as in natural habitat conservation, setting the excavation time interval for resource regeneration and the substitution of cultivated for wild plants.     

Benthic habitat and fish assemblage structure from shallow to mesophotic depths in a storm-impacted marine protected area

Coral Reefs - Baseline ecological studies of mesophotic coral ecosystems are lacking in the equatorial Indo-West Pacific region where coral reefs are highly threatened by anthropogenic and...     

Seasonal response of fish assemblages to habitat fragmentation caused by an impoundment in a Neotropical river

Changes in fish assemblages between the zones above and below Funil dam in Southeastern Brazil were investigated to evaluate the possible impacts of this impoundment in two contrasting seasons: summer/wet and winter/dry. We expect differences in fish assemblage structure and in environmental conditions between seasons and between the reservoir and the zone downriver of the dam. A total of 3,579 individuals comprising 38 species, including six non-natives, were collected. As expected, the comparatively high habitat complexity and water flow regime of the downriver zone favored a richer and more abundant fish assemblage compared with the reservoir, especially in the wet season. In this period, water covers part of the riparian vegetation, increasing habitat availability and nutrient input. Additionally, the dam prevents upriver migration of rheophilics fish species such as the Characiformes Prochilodus lineatus and Leporinus copelandii, and the Siluriformes Pimelodus fur and Pimelodus maculatus, thus increasing shoals below the dam. Although the reservoir represents a simplified ecosystem highly influenced by non-native top predator species (e.g. the Perciformes Cichla kelberi and Plagioscion squamosissimus), seasonal processes (e.g. water level fluctuations and flood pulses) seem to play a role in structuring of the fish assemblage. Environmental variables, mainly turbidity, temperature, and conductivity were significantly associated to spatial-temporal patterns of fish assemblage. In this freshwater tropical reservoir, the spatial scale, rather than the seasonal changes in environmental variables, was the dominant factor structuring fish assemblage in the reservoir and in the zone downriver of the dam.