Population Demography and Herbivory of Trillium Grandiflorum

Numerous pedicellate and sessile Trillium species are endemic to eastern North America, where white-tailed deer (Odocoileus virginianus) populations have been growing in recent decades. Deer feed on Trillium plants, and because they often consume all leaves and flowers, the photosynthetic capacity of browsed plants is greatly diminished. To determine if deer can influence Trillium population dynamics, we review two recent studies that applied matrix population models to understand how deer browsing affects Trillium grandijlorum. Research conducted in the Great Lakes region indicated Trillium populations in which 6-12% plants were browsed declined 3.6% per year. Simulations show that with additional browsing, the rate of population decline accelerates. Similar research conducted in the Appalachian plateau region by a different researcher yielded nearly identical results. We apply insights from these matrix population models to two additional conservation problems in Trillium: unsustainable collecting of wild plants and forest fragmentation. Because other Trillium in the eastern United States are similar morphologically and ecologically, our results from Trillium grandiflorum might be generalized to apply to other members of the genus

Phylogeny, Adaptive Radiation, and Historical Biogeography of Bromeliaceae Inferred from ndhF Sequence Data

Cladistic analysis of ndhF sequences identifies eight major bromeliad clades arranged in ladderlike fashion. The traditional subfamilies Tillandsioideae and Bromelioideae are monophyletic, but Pitcairnioideae are paraphyletic, requiring the description of four new subfamilies, recircumscription of Pitcairnioideae and Navioideae, the sinking of Ayensua, and description of the new genus Sequencia. Brocchinioideae are basalmost, followed by Lindmanioideae, both restricted to the Guayana Shield. Next is an unresolved trichotomy involving Hechtioideae from Central America, Tillandsioideae, and the remaining bromeliads in subfamilies Navioideae, Pitcairnioideae, Puyoideae, and Bromelioideae. Bromeliads arose as C3 terrestrial plants on moist infertile sites in the Guayana Shield roughly 70 Mya, spread centripetally in the New World, and reached tropical West Africa (Pitcairnia feliciana) via long-distance dispersal about 10 Mya. Modern lineages began to diverge from each other 19 Mya and invaded drier areas in Central and South America beginning 15 Mya, coincident with a major adaptive radiation involving the repeated evolution of epiphytism, CAM photosynthesis, impounding leaves, several features of leaf/trichome anatomy, and accelerated diversification at the generic level. This ‘‘bromeliad revolution’’ occurred after the uplift of the northern Andes and shift of the Amazon to its present course. Epiphytism may have accelerated speciation by increasing ability to colonize along the length of the Andes, while favoring the occupation of a cloud-forest landscape frequently dissected by drier valleys. Avian pollination (mainly by hummingbirds) evolved at least twice ca. 13 Mya; entomophily was ancestral. Hechtia, Abromeitiella–Deuterocohnia–Dyckia–Encholirium, and Puya exhibit a remarkable pattern of concerted convergence in six anatomical and physiological leaf traits adapted to drought

Phylogenetic Relationships of Monocots Based on the Highly Informative Plastid Gene ndhF

We used ndhF sequence variation to reconstruct relationships across 282 taxa representing 78 monocot families and all 12 orders. The resulting tree is highly resolved and places commelinids sister to Asparagales, with both sister to Liliales—Pandanales in the strict consensus; Pandanales are sister to Dioscoreales in the bootstrap majority-rule tree, just above Petrosaviales. Acorales are sister to all other monocots, with Alismatales sister to all but Acorales. Relationships among the four major clades of commelinids remain unresolved. Relationships within orders are consistent with those based on rbcL, alone or in combination with atpB and 18S nrDNA, and generally better supported: ndhF contributes more than twice as many informative characters as rbcL, and nearly as many as rbcL, atpB, and 18S nrDNA combined. Based on functional arguments, we hypothesized that net venation and fleshy fruits should both evolve—and thus undergo concerted convergence—in shaded habitats, and revert to parallel venation and dry, passively dispersed fruits in open, sunny habitats. Our data show that net venation arose at least 26 times and disappeared 9 times, whereas fleshy fruits arose 22 times and disappeared 11 times. Both traits arose together at least 15 times and disappeared together 5 times. They thus show a highly significant pattern of concerted convergence (P \u3c 10-9) and are each even more strongly associated with shaded habitats (P \u3c 10-10 to 10-23); net venation is also associated, as predicted, with broad-leaved aquatic plants. Exceptions to this pattern illustrate the importance of other selective constraints and phylogenetic inertia

A Quantitative Analysis of Kalandars and Captive Bears in Pakistan

In 2013, the Bioresource Research Centre (Islamabad, Pakistan) conducted a comprehensive census of the remaining dancing and bear-baiting bears in Pakistan. This involved locating and counting the actual involved bears and bear keepers (kalandars), collecting detailed socio-economic data from the bear-keepers, and identifying attitudes and key drivers behind this livelihood. This report summarizes the findings from the census, reveals relationships in the data that are not immediately apparent, and identifies potential leverage points for ongoing campaign efforts

Assessment of Habitat, Threats and Population Status for the Federally-endangered Wetland Sedge, Northeastern Bulrush, Scirpus ancistrochaetus

Background/Question/Methods Northeastern bulrush, Scirpus ancistrochaetus, is a federally-endangered emergent sedge that grows in small, temporary palustrine wetlands. In 2007 and 2008, we performed surveys of 81 wetlands on public lands in Pennsylvania to characterize the habitat, to document population status, and to assess threats. At each wetland, we measured areal extent, density of stems, and number of flowering culms of S. ancistrochaetus. We also measured habitat variables including percent tree canopy cover, presence of invasive species, level of deer activity and size of wetland. Additionally, we collected leaves for analysis of genetic diversity using RAPDs and microsatellite markers. We performed pairwise correlations to examine relationships among habitat and S. ancistrochaetus variables. For the 54 sites where previous data existed, we also made a comparative evaluation of the population trajectory. Results/Conclusions Wetlands containing S. ancistrochaetus were found at elevations between 240 and 640 m, with a median of 511 m and ranged from 90 m2 to 6500 m2 in area, with a median of 563 m2. Percent tree canopy cover was negatively correlated with stem density, areal extent of population, and proportion of flowering stems. Wetland area was positively related to these variables, most likely due to fact that larger wetlands had lower percent cover and more open water. The invasive species Phalaris arundinacea was present in 8% of wetlands, and is the probable cause of extirpation at one site. Invasive Microstegium vimineum was a possible threat in 20% of wetlands. Deer trampling or browsing was recorded in 40% of wetlands, with more significant impacts during the fall. Bear activity, including wallows, was observed in 16% of wetlands. For the 54 populations with previous data, 33% were stable, 11% increased, 28% decreased, and 26% suffered severe declines or were completely extirpated. Clearly, more management and monitoring is needed to effectively conserve this species, as over 50% of populations experienced declines. Existing managment recommendations at each wetland include no-cut buffer zones. Our top recommendation for management is to cut in these buffer zones, reducing tree canopy cover to 50%. At some sites, protection from animal activity and control of invasive plant species may be warranted. Preliminary genetic diversity analyses indicate fairly low diversity in this clonal species; additional work will investigate diversity among and within wetlands in greater detail. This information will be used to target sites for protection and management in a way that preserves the full complement of genetic diversity in this species

Assessment of Habitat, Threats and Population Status for the Federally-endangered Wetland Sedge, Northeastern Bulrush, Scirpus ancistrochaetus

Background/Question/Methods Northeastern bulrush, Scirpus ancistrochaetus, is a federally-endangered emergent sedge that grows in small, temporary palustrine wetlands. In 2007 and 2008, we performed surveys of 81 wetlands on public lands in Pennsylvania to characterize the habitat, to document population status, and to assess threats. At each wetland, we measured areal extent, density of stems, and number of flowering culms of S. ancistrochaetus. We also measured habitat variables including percent tree canopy cover, presence of invasive species, level of deer activity and size of wetland. Additionally, we collected leaves for analysis of genetic diversity using RAPDs and microsatellite markers. We performed pairwise correlations to examine relationships among habitat and S. ancistrochaetus variables. For the 54 sites where previous data existed, we also made a comparative evaluation of the population trajectory. Results/Conclusions Wetlands containing S. ancistrochaetus were found at elevations between 240 and 640 m, with a median of 511 m and ranged from 90 m2 to 6500 m2 in area, with a median of 563 m2. Percent tree canopy cover was negatively correlated with stem density, areal extent of population, and proportion of flowering stems. Wetland area was positively related to these variables, most likely due to fact that larger wetlands had lower percent cover and more open water. The invasive species Phalaris arundinacea was present in 8% of wetlands, and is the probable cause of extirpation at one site. Invasive Microstegium vimineum was a possible threat in 20% of wetlands. Deer trampling or browsing was recorded in 40% of wetlands, with more significant impacts during the fall. Bear activity, including wallows, was observed in 16% of wetlands. For the 54 populations with previous data, 33% were stable, 11% increased, 28% decreased, and 26% suffered severe declines or were completely extirpated. Clearly, more management and monitoring is needed to effectively conserve this species, as over 50% of populations experienced declines. Existing managment recommendations at each wetland include no-cut buffer zones. Our top recommendation for management is to cut in these buffer zones, reducing tree canopy cover to 50%. At some sites, protection from animal activity and control of invasive plant species may be warranted. Preliminary genetic diversity analyses indicate fairly low diversity in this clonal species; additional work will investigate diversity among and within wetlands in greater detail. This information will be used to target sites for protection and management in a way that preserves the full complement of genetic diversity in this species

Comparison of Genetic Population Structure of Endangered Scirpus ancistrochaetus using Two Methods

Background/Question/Methods Northeastern bulrush, Scirpus ancistrochaetus, is a federally-endangered emergent sedge, found in wetlands in the Northeast, with a majority of populations in Pennsylvania. To date, there is no information on the population genetics of this species. Until we have an understanding of the genetic diversity of this species at local and regional scales, we will not know the extent to which fluctuations in population sizes due to environmental impacts such as climate change, hydrologic changes and increasing canopy cover will negatively impact the conservation of genetic resources in the field. With over 50% of populations in need of management, population genetics studies can be used to prioritize key areas for management and monitoring. The goal of this research is to characterize the genetic population structure of this species using two methods. We collected leaf samples from 26 sites in Pennsylvania, 9 sites in the southern range of S.ancistrochaetus (Maryland, Virginia and West Virginia) and 13 sites in the northern range of S. ancistrochaetus (Vermont and New Hampshire). Using DNA sequencing, we identified several SNPs (single nucleotide polymorphisms) that showed variation among the S. ancistrochaetus populations. The advantage of SNPs and other sequence data is reproducibility, robustness to sample variation and ease of screening once they are detected. At the same time, we are utilizing RAPDs (Randomly Amplified Polymorphic DNA) to provide additional information on population genetics at a subset of sites. The use of RAPDs is considered less reliable and robust, yet is easy and relatively inexpensive. We then compared the resultant genetic structures created from each of the two methods. Results/Conclusions Within-population genetic variation is low, as predicted for this clonal species. For between-population variation, genetic structures from methods concur for the most part, with slightly more variation revealed by the RAPDs. The use of RAPDs may therefore be a viable technique to examine genetic diversity in this species in some cases, such as when resources are limited. Some populations displayed genetic uniqueness; this information may be used to target sites for protection and management in a way that preserves the full complement of genetic diversity in this species

Comparison of Genetic Population Structure of Endangered Scirpus ancistrochaetus using Two Methods

Background/Question/Methods Northeastern bulrush, Scirpus ancistrochaetus, is a federally-endangered emergent sedge, found in wetlands in the Northeast, with a majority of populations in Pennsylvania. To date, there is no information on the population genetics of this species. Until we have an understanding of the genetic diversity of this species at local and regional scales, we will not know the extent to which fluctuations in population sizes due to environmental impacts such as climate change, hydrologic changes and increasing canopy cover will negatively impact the conservation of genetic resources in the field. With over 50% of populations in need of management, population genetics studies can be used to prioritize key areas for management and monitoring. The goal of this research is to characterize the genetic population structure of this species using two methods. We collected leaf samples from 26 sites in Pennsylvania, 9 sites in the southern range of S.ancistrochaetus (Maryland, Virginia and West Virginia) and 13 sites in the northern range of S. ancistrochaetus (Vermont and New Hampshire). Using DNA sequencing, we identified several SNPs (single nucleotide polymorphisms) that showed variation among the S. ancistrochaetus populations. The advantage of SNPs and other sequence data is reproducibility, robustness to sample variation and ease of screening once they are detected. At the same time, we are utilizing RAPDs (Randomly Amplified Polymorphic DNA) to provide additional information on population genetics at a subset of sites. The use of RAPDs is considered less reliable and robust, yet is easy and relatively inexpensive. We then compared the resultant genetic structures created from each of the two methods. Results/Conclusions Within-population genetic variation is low, as predicted for this clonal species. For between-population variation, genetic structures from methods concur for the most part, with slightly more variation revealed by the RAPDs. The use of RAPDs may therefore be a viable technique to examine genetic diversity in this species in some cases, such as when resources are limited. Some populations displayed genetic uniqueness; this information may be used to target sites for protection and management in a way that preserves the full complement of genetic diversity in this species

Data from: Mito-nuclear discord in six congeneric lineages of Holarctic ducks (genus Anas)

Many species have Holarctic distributions that extend across Europe, Asia, and North America. Most genetics research on these species has examined only mitochondrial (mt) DNA, which has revealed wide variance in divergence between Old World (OW) and New World (NW) populations, ranging from shallow, unstructured genealogies to deeply divergent lineages. In this study, we sequenced 20 nuclear introns to test for concordant patterns of OW-NW differentiation between mtDNA and nuclear (nu) DNA for six lineages of Holarctic ducks (genus Anas). Genetic differentiation for both marker types varied widely among these lineages (idiosyncratic population histories), but mtDNA and nuDNA divergence within lineages was not significantly correlated. Moreover, compared to the association between mtDNA and nuDNA divergence observed among different species, OW-NW nuDNA differentiation was generally lower than mtDNA divergence, at least for lineages with deeply divergent mtDNA. Furthermore, coalescent estimates indicated significantly higher rates of gene flow for nuDNA than mtDNA for four of the six lineages. Thus, Holarctic ducks show prominent mito-nuclear discord between OW and NW populations, and we reject differences in sorting rates as the sole cause of the within-species discord. Male-mediated intercontinental gene flow is likely a leading contributor to this discord, although selection could also cause elevated mtDNA divergence relative to weak nuDNA differentiation. The population genetics of these ducks contribute to growing evidence that mtDNA can be an unreliable indicator of stage of speciation, and that more holistic approaches are needed for species delimitation