Spatial processes in ecology and evolution, and implications for conservation

Habitat loss and fragmentation is the main culprit behind the current decline in biodiversity. The estimated current rate of extinction is two or three orders of magnitude higher than the background extinction rate. This thesis analyzes existing data and develops models to improve our understanding of the role of spatial processes in the dynamics of populations and communities. This work is focused on the features of habitat destruction that causes decline of biodiversity as well as the traits that make species vulnerable to habitat loss. First, I attempt to infer relationships between spatial heterogeneity, rate of diversification (speciation and extinction), and the dynamics of geographical ranges from a reconstructed phylogeny. I build a flexible comparative method to analyze adaptive radiation and range dynamics that extends the current models in two directions by allowing more than two regions and by assuming diversity-dependent diversification rates. In a five-region system stimulated by the biogeography of Madagascar, processes that increase and decrease diversity are strongly correlated. Therefore, it is not possible to estimate independently region-specific speciation and extinction rates, though their ratios can be successfully estimated. When applied to Malagasy dung beetles, we found that diversification rate is highest in the northern (very heterogeneous) and lowest in the southern (most homogeneous) parts of Madagascar. Thus it appears that landscape heterogeneity promotes diversification and thus biodiversity. The two other chapters investigate the consequences of habitat loss and fragmentation for generalist and specialist species. We aim to understand how generalist and specialist species respond to habitat loss and fragmentation. In particular, we ask why generalist species often increase in abundance following an intermediate level of habitat destruction. I develop a modular modeling approach that allows one to switch on and off various mechanisms as needed. This approach one to assess the marginal and joint effects of different mechanisms by comparing model outcomes. Our analyses confirm that a high level of specialization leads to high sensitivity to habitat loss and fragmentation. When landscape quality is high, specialists are competitively superior, but when landscape degrades, generalists gradually become superior. In previous models, competitive hierarchy is usually thought to be an intrinsic property of species, but we show that a shift in competitive capacity is caused by extrinsic factors. Comparing deterministic versus stochastic models, we find that a key extrinsic factor is increase in demographic stochasticity in degraded landscapes that affects specialists more than generalists. In the third chapter, I ask about the role of large- scale habitat corridor for biodiversity conservation. We analyzed a community of 300 species belonging to 6 taxonomic groups inhabiting more than 2000 km2 forest, composed of two large national parks in Madagascar, Ranomafana and Andringitra, and connected by a corridor. We found that in 2000 the corridor was still functional, but since then it has degraded substantially and may lose its corridor function in the coming decades. Our spatially realistic simulations show that species with passive mode of dispersal suffer the most from corridor destruction. This thesis emphasizes the role of different mechanisms that should be considered while analyzing species responses to changes in habitat structure. The most important ones are the mode of dispersal, ecological specialization, temporal and spatial stochasticity, and competition. As such, tropical regions, like Madagascar, are in double trouble due to high ecological specialization of most species and high rates of habitat destruction. Effective measures need to be enforced to ameliorate the conditions within and outside protected areas so they can truly enhance biodiversity protection.Biodiversiteetin nykyinen vähenemisnopeus on samaa suuruusluokkaa kuin aiemmissa sukupuuttoaalloissa. Yksi päätekijöistä biodiversiteetin vähenemisen takana on ihmisen aiheuttama elinympäristöjen väheneminen. Tässä väitöskirjassa analysoin sekä empiirisiä aineistoja että matemaattisia malleja. Tavoitteenani on lisätä ymmärrystä elinympäristöjen rakenteen merkityksestä lajiyhteisöille, sekä siitä minkälaiset lajit kärsivät erityisesti niiden elinympäristöjen vähenemisestä. Tässä väitöskirjassa kehittämäni matemaattiset mallit ottavat elinympäristöjen spatiaalisen rakenteen huomioon ekologisten ja evolutiivisten prosessien mallintamisessa. Ensimmäisessä osatyössä käytän tilastollista mallinnusta etsiäkseni yhteyksiä ympäristön heterogeenisuuden ja lajiutumisnopeuden välille. Toisessa osatyössä käytän matemaattisia malleja ymmärtääkseni miten elinympäristöjen häviäminen ja pirstoutuminen vaikuttaa kilpaileviin lajeihin joiden erikoistumisaste niiden ympäristövaatimusten suhteen on erilainen. Viimeisessä osatyössä tarkastelen konkreettista esimerkkiä elinympäristön häviämisestä ja pirstoutumisesta, tavoitteena selvittää miten Madagaskarin kaakkoisosassa oleva Ranomafanan ja Andrinitran kansallispuistot yhdistävä metsäkäytävä edistää näiden puistojen biodiversiteetin säilymistä. Väitöskirjan tulokset osoittavat että ekolokeroltaan kapeat eli elinympäristövaatimustensa suhteen erikoistuneet lajit ovat erityisen herkkiä elinympäristön häviämiselle. Kun elinympäristön määrä vähenee, vähemmän erikoistuneet lajit saavat etua lajien välisessä kilpailussa, ja erikoistuneita lajeja uhkaa sukupuutto. Väitöskirjan tulokset osoittavat myös sen että passiivisesti esim. tuulen mukana leviävät lajit ovat herkempiä elinympäristön häviämiselle kuin aktiivisesti liikkuvat lajit. Ranomafanan ja Andringitran välinen metsäkäytävä oli hyvässä kunnossa vielä vuonna 2000, mutta sen tila on huononemassa nopeasti. Jos käytävän nykyinen pirstoutumistahti jatkuu, sitä ei ole enää vuonna 2090. Madagaskarin lantakuoriaisten fylogeneettinen analyysi osoittaa että lajiutumisnopeus on ollut suurin heterogeenisissa ympäristöissä. Tämän väitöskirjan menetelmällinen osuus osoittaa sen että ympäristön rakenteen melko realistinen huomiointi on mahdollista ekologian ja evoluutiobiologian matemaattisessa mallintamisessa. Väitöskirjan tulokset korostavat lajin ekolokeron leveyden, dispersaalin, ja lajien välisen kilpailun vaikutusta siihen miten lajit vastaavat elinympäristöjen vähenemiseen. Ympäristön heterogeenisuus lisää lajiutumisnopeutta ja mahdollistaa lajien erikoistumisen. Madagaskarin kaltaisessa paikassa, jossa on paljon ekolokeroltaan kapeita lajeja, ja jossa elinympäristöt häviävät nopeaa tahtia, biodiversiteetin suojelu on erityisen haastavaa

Regeneration Strategies and Forest Resilience to Changing Fire Regimes: Insights From a Goldilocks Model

Disturbances are ubiquitous in ecological systems, and species have evolved a range of strategies to resist or rebound following disturbance. Understanding how the presence and complementarity of regeneration traits will affect community responses to disturbance is increasingly urgent as disturbance regimes shift beyond their historical ranges of variability. We define disturbance niche as a species\u27 fitness across a range of disturbance sizes and frequencies that can reflect the fundamental or realized niche, that is, whether the species occurs alone or with other species. We developed a model of intermediate complexity (i.e., a Goldilocks model) to infer the disturbance niche. We parameterized the model for subalpine forests in Yellowstone National Park (USA) adapted to infrequent stand-replacing fires and included the three major tree-regeneration strategies: (1) obligate seeders that rely on ex situ seeding into burned areas (non-serotinous lodgepole pine, Pinus contorta var. latifola), (2) obligate seeders that depend on in situ seedbanks (serotinous lodgepole pine, Pinus contorta var. latifola), and (3) species that can resprout from surviving roots following fire (quaking aspen, Populus tremuloides). Our results showed which regeneration strategies increase or decrease in prevalence as fire rotation declines. Non-serotinous pines were extirpated when fire rotation was below 50 years in a monoculture and 100 years in a mixed forest; serotinous pines were extirpated when fire rotation was below 20 years; and aspen was extirpated when fire rotation fell below 6 years. The fundamental and realized disturbance niches pinpointed the key mechanisms limiting regeneration for each strategy, namely, increasing fire size for non-serotinous pine (ex situ seeders), decreasing fire frequency for serotinous pine (in situ seeders), and interspecific competition for aspen (resprouters). In a mixed forest, the three regeneration strategies were complementary and each dominated at different combinations of fire size and frequency. Consequently, diversity of regeneration strategies enhanced forest resilience to declining fire rotations. Despite its simplicity, our Goldilocks model produced realistic dynamics and could be readily adapted to other disturbance-prone ecosystems to explore the generality of these results. The disturbance niche is a key concept for anticipating community resilience to changing disturbance regimes

Uncertainty in coprophilous fungal spore concentration estimates

The abundance of coprophilous (dung-inhabiting) fungal spores (CFS) in sedimentary records is an increasingly popular proxy for past megaherbivore abundance that is used to study megaherbivore-vegetation interactions, timing of megaherbivore population declines and extinctions, and the introduction of domesticated herbivores. This method often relies on counting CFS alongside pollen and tracers of known concentration such as exotic pollen or synthetic microspherules. Prior work has encouraged reporting CFS abundances as accumulation rates (spores/unit2/year) or concentration (spores/unit3) instead of percentages relative to the total pollen abundance, because CFS percentages can be sensitive to fluctuations in pollen influx. In this work, we quantify the uncertainty associated with estimating concentration values at different total counts and find that high uncertainty is associated with concentration estimates using low to moderate total counts (n = 20 to 200) of individual fungal spore types and tracers. We also demonstrate the effect of varying tracer proportions, and find that larger tracer proportions result in narrower confidence intervals. Finally, the probability of encountering a CFS spore from a specific taxon occurring in moderate concentrations (1,000 spores/unit2) dramatically decreases after a low tracer count (∼50). The uncertainties in concentration estimates caused by calculating tracer proportion are a likely cause of the high observed variance in many CFS time series, especially when CFS or tracer concentrations are low. Thus, we recommend future CFS studies increase counts and report the uncertainty surrounding concentration values. For some records, reporting spore data as presence/absence rather than concentrations or counts is preferable, such as when performing high counts is not feasible.Fil: Perrotti, Angelina G.. University Brown; Estados UnidosFil: Ramiadantsoa, Tanjona. University of Wisconsin; Estados UnidosFil: OKeefe, Jennifer. Morehead State University; Estados UnidosFil: Nuñez Otaño, Noelia Betiana. Universidad Autónoma de Entre Ríos. Facultad de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Phylogenetic comparative method for geographical radiation

Phylogeny can provide information about the processes that have shaped extant diversity. Here, we complement existing comparative phylogenetic methods by developing a model that couples diversity-dependent diversification rate and range dynamics. Unlike many models, we used Approximate Bayesian Computation to fit the model to the data. We validated the inference by estimating known parameter values from simulated data, and found that within-region speciation and extinction rates cannot be simultaneously estimated most likely due to correlations among parameter values. Since the model can estimate a diversification rate, we applied the model to a monophyletic lineage of 74 species of dung beetles (Canthonini: Nanos and Apotolamprus) endemic to Madagascar. The estimated diversification rate is clearly higher in northern than in eastern or western Madagascar. The current species richness is highest in North where complex topography and a mixture of biomes likely favour ecological diversification. The approach we have developed here is a step towards examining weaknesses and strengths of phylogenetic comparative methods in an explicit spatial context. Further development and testing of the model is needed before its routine application to empirical data.Peer reviewe

Large-Scale Habitat Corridors for Biodiversity Conservation : A Forest Corridor in Madagascar

In biodiversity conservation, habitat corridors are assumed to increase landscape-level connectivity and to enhance the viability of otherwise isolated populations. While the role of corridors is supported by empirical evidence, studies have typically been conducted at small spatial scales. Here, we assess the quality and the functionality of a large 95-km long forest corridor connecting two large national parks (416 and 311 km(2)) in the southeastern escarpment of Madagascar. We analyze the occurrence of 300 species in 5 taxonomic groups in the parks and in the corridor, and combine high-resolution forest cover data with a simulation model to examine various scenarios of corridor destruction. At present, the corridor contains essentially the same communities as the national parks, reflecting its breadth which on average matches that of the parks. In the simulation model, we consider three types of dispersers: passive dispersers, which settle randomly around the source population; active dispersers, which settle only in favorable habitat; and gap-avoiding active dispersers, which avoid dispersing across non-habitat. Our results suggest that long-distance passive dispersers are most sensitive to ongoing degradation of the corridor, because increasing numbers of propagules are lost outside the forest habitat. For a wide range of dispersal parameters, the national parks are large enough to sustain stable populations until the corridor becomes severely broken, which will happen around 2065 if the current rate of forest loss continues. A significant decrease in gene flow along the corridor is expected after 2040, and this will exacerbate the adverse consequences of isolation. Our results demonstrate that simulation studies assessing the role of habitat corridors should pay close attention to the mode of dispersal and the effects of regional stochasticity.Peer reviewe

Predicting range shifts for critically endangered plants : is habitat connectivity irrelevant or necessary?

Climate and land-cover change will directly impact future species distributions, leading to range expansions, contractions and local extinctions. However, assessments of future range shifts rarely account for the capacity of the landscape matrix to facilitate species dispersals. Here, we assessed future range shifts for a suite of critically endangered plants in Madagascar. We quantified habitat connectivity using a least cost path model that captured the potential of species to disperse within fragmented landscapes. Next, we constructed three scenarios representing landscapes impacted by climate-only, climate and land-cover change, as well as habitat connectivity. We modelled species distributions using a hierarchical Bayesian framework and measured future range shifts using three spatial indices: net-change, range distance and elevation change. Our results show that the median range shift due to contractions increased by 25% under the climate-only scenario compared with the connectivity scenario. Habitat connectivity is predicted to limit range shifts due to contractions, while increasing shifts due to expansions for many of the endangered and critically endangered plants on Madagascar. However, at least one-third of critically endangered and 50% of endangered plants are expected to experience range contractions and upslope displacement under all scenarios, suggesting that even with habitat connectivity the range of some species may still contract. Despite that finding, our study suggests that including connectivity in range shift models is crucial for developing a relevant connectivity conservation plan, since future climate or climate and land-cover change models do not adequately represent species' potential to reach safe sites

Habitat fragmentation increases overall richness, but not of habitat-dependent species

Debate rages as to whether habitat fragmentation leads to the decline of biodiversity once habitat loss is accounted for. Previous studies have defined fragmentation variously, but research needs to address “fragmentation per se,” which excludes confounding effects of habitat loss. Our study controls for habitat area and employs a mechanistic multi-species simulation to explore processes that may lead some species groups to be more or less sensitive to fragmentation per se. Our multi-land-cover, landscape-scale, individual-based model incorporates the movement of generic species, each with different land cover preferences. We investigate how fragmentation per se changes diversity patterns; within (alpha), between (beta) and across (gamma) patches of a focal-land-cover, and if this differs among species groups according to their specialism and dependency on this focal-land-cover. We defined specialism as the increased competitive ability of specialists in suitable habitat and decreased ability in less suitable land covers compared to generalist species. We found fragmentation per se caused an increase in gamma diversity in the focal-land-cover if we considered all species regardless of focal-land-cover preference. However, critically for conservation, the gamma diversity of species for whom the focal land cover is suitable habitat declined under fragmentation per se. An exception to this finding occurred when these species were specialists, who were unaffected by fragmentation per se. In general, focal-land-cover species were under pressure from the influx of other species, with fragmentation per se leading to a loss of alpha diversity not compensated for by increases in beta diversity and, therefore, gamma diversity fell. The specialist species, which were more competitive, were less affected by the influx of species and therefore alpha diversity decreased less with fragmentation per se and beta diversity compensated for this loss, meaning gamma diversity did not decrease. Our findings help to inform the fragmentation per se debate, showing that effects on biodiversity can be negative or positive, depending on species’ competitive abilities and dependency on the fragmented land cover. Such differences in the effect of fragmentation per se would have important consequences for conservation. Focusing conservation efforts on reducing or preventing fragmentation in areas with species vulnerable to fragmentation

Advancing transdisciplinary research on Madagascar's grassy biomes to support resilience in ecosystems and livelihoods

Grassy biomes (savanna and grasslands) are globally extensive and host a unique biodiversity that is of central importance to human livelihoods. We focus here on the island of Madagascar—a microcosm of the global tropics, covered in 80% grassy biomes—to illustrate how transdisciplinary approaches to research can clarify ecosystem dynamics, from evolutionary history to human land use. Research on Madagascar's human-environment interactions has sparked debates about the role of past and current land use in shaping grassy biomes (e.g., pastoralism, cultivation, fire use). These debates echo those in other regions globally, and highlight obstacles to understanding and supporting both ecosystem and livelihood resilience. Like many tropical biodiversity hotspots, Madagascar faces converging challenges that can be aided by transdisciplinary research, including food and health insecurity, economic inequities, biodiversity loss, climate change, land conversion, and limited resource access. We present a framework to guide transdisciplinary research centered on improved understanding and management of grassy biomes on Madagascar by: (1) establishing a globally common terminology; (2) summarizing data contributions and scientific knowledge gaps relating to Madagascar's grassy biomes; (3) identifying priority research questions for Madagascar with applicability in other regions; and (4) highlighting transdisciplinary, inclusive approaches to research that can co-benefit people and the ecosystems with which they interact

Uncertainty in coprophilous fungal spore concentration estimates

The abundance of coprophilous (dung-inhabiting) fungal spores (CFS) in sedimentary records is an increasingly popular proxy for past megaherbivore abundance that is used to study megaherbivore-vegetation interactions, timing of megaherbivore population declines and extinctions, and the introduction of domesticated herbivores. This method often relies on counting CFS alongside pollen and tracers of known concentration such as exotic pollen or synthetic microspherules. Prior work has encouraged reporting CFS abundances as accumulation rates (spores/unit2/year) or concentration (spores/unit3) instead of percentages relative to the total pollen abundance, because CFS percentages can be sensitive to fluctuations in pollen influx. In this work, we quantify the uncertainty associated with estimating concentration values at different total counts and find that high uncertainty is associated with concentration estimates using low to moderate total counts (n = 20 to 200) of individual fungal spore types and tracers. We also demonstrate the effect of varying tracer proportions, and find that larger tracer proportions result in narrower confidence intervals. Finally, the probability of encountering a CFS spore from a specific taxon occurring in moderate concentrations (1,000 spores/unit2) dramatically decreases after a low tracer count (∼50). The uncertainties in concentration estimates caused by calculating tracer proportion are a likely cause of the high observed variance in many CFS time series, especially when CFS or tracer concentrations are low. Thus, we recommend future CFS studies increase counts and report the uncertainty surrounding concentration values. For some records, reporting spore data as presence/absence rather than concentrations or counts is preferable, such as when performing high counts is not feasible.</jats:p