Marine foundation species shifting ranges and genetic baselines

This thesis revealed the most importance factors shaping the distribution, abundance and genetic diversity of four marine foundation species. Environmental conditions, particularly sea temperatures, nutrient availability and ocean waves, played a primary role in shaping the spatial distribution and abundance of populations, acting on scales varying from tens of meters to hundreds of kilometres. Furthermore, the use of Species Distribution Models (SDMs) with biological records of occurrence and high-resolution oceanographic data, allowed predicting species distributions across time. This approach highlighted the role of climate change, particularly when extreme temperatures prevailed during glacial and interglacial periods. These results, when combined with mtDNA and microsatellite genetic variation of populations allowed inferring for the influence of past range dynamics in the genetic diversity and structure of populations. For instance, the Last Glacial Maximum produced important shifts in species ranges, leaving obvious signatures of higher genetic diversities in regions where populations persisted (i.e., refugia). However, it was found that a species’ genetic pool is shaped by regions of persistence, adjacent to others experiencing expansions and contractions. Contradicting expectations, refugia seem to play a minor role on the re(colonization) process of previously eroded populations. In addition, the available habitat area for expanding populations and the inherent mechanisms of species dispersal in occupying available habitats were also found to be fundamental in shaping the distributions of genetic diversity. However, results suggest that the high levels of genetic diversity in some populations do not rule out that they may have experienced strong genetic erosion in the past, a process here named shifting genetic baselines. Furthermore, this thesis predicted an ongoing retraction at the rear edges and extinctions of unique genetic lineages, which will impoverish the global gene pool, strongly shifting the genetic baselines in the future.

Species richness declines and biotic homogenization have slowed down for NW-European pollinators and plants

Concern about biodiversity loss has led to increased public investment in conservation. Whereas there is a widespread perception that such initiatives have been unsuccessful, there are few quantitative tests of this perception. Here, we evaluate whether rates of biodiversity change have altered in recent decades in three European countries (Great Britain, Netherlands and Belgium) for plants and flower visiting insects. We compared four 20-year periods, comparing periods of rapid land-use intensification and natural habitat loss (1930–1990) with a period of increased conservation investment (post-1990). We found that extensive species richness loss and biotic homogenisation occurred before 1990, whereas these negative trends became substantially less accentuated during recent decades, being partially reversed for certain taxa (e.g. bees in Great Britain and Netherlands). These results highlight the potential to maintain or even restore current species assemblages (which despite past extinctions are still of great conservation value), at least in regions where large-scale land-use intensification and natural habitat loss has ceased.

Species-specific responses of Late Quaternary megafauna to climate and humans

Despite decades of research, the roles of climate and humans in driving the dramatic extinctions of large-bodied mammals during the Late Quaternary period remain contentious. Here we use ancient DNA, species distribution models and the human fossil record to elucidate how climate and humans shaped the demographic history of woolly rhinoceros, woolly mammoth, wild horse, reindeer, bison and musk ox. We show that climate has been a major driver of population change over the past 50,000 years. However, each species responds differently to the effects of climatic shifts, habitat redistribution and human encroachment. Although climate change alone can explain the extinction of some species, such as Eurasian musk ox and woolly rhinoceros, a combination of climatic and anthropogenic effects appears to be responsible for the extinction of others, including Eurasian steppe bison and wild horse. We find no genetic signature or any distinctive range dynamics distinguishing extinct from surviving species, emphasizing the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change.

Using Africa’s protected area network to estimate the global population of a threatened and declining species: a case study of the critically endangered White-headed Vulture Trigonoceps occipitalis

The White-headed Vulture Trigonoceps occipitalis (WhV) is uncommon and largely restricted to protected areas across its range in sub-Saharan Africa. We used the World Database on Protected Areas to identify protected areas (PAs) likely to contain White-headed Vultures. Vulture occurrence on road transects in Southern, East, and West Africa was adjusted to nests per km2 using data from areas with known numbers of nests and corresponding road transect data. Nest density was used to calculate the number of WhV nests within identified PAs and from there extrapolated to estimate the global population. Across a fragmented range, 400 PAs are estimated to contain 1893 WhV nests. Eastern Africa is estimated to contain 721 nests, Central Africa 548 nests, Southern Africa 468 nests, and West Africa 156 nests. Including immature and nonbreeding birds, and accounting for data deficient PAs, the estimated global population is 5475 - 5493 birds. The identified distribution highlights are alarming: over 78% (n = 313) of identified PAs contain fewer than five nests. A further 17% (n = 68) of PAs contain 5 - 20 nests and 4% (n = 14) of identified PAs are estimated to contain >20 nests. Just 1% (n = 5) of PAs are estimated to contain >40 nests; none is located in West Africa. Whilst ranging behavior of WhVs is currently unknown, 35% of PAs large enough to hold >20 nests are isolated by more than 100 km from other PAs. Spatially discrete and unpredictable mortality events such as poisoning pose major threats to small localized vulture populations and will accelerate ongoing local extinctions. Apart from reducing the threat of poisoning events, conservation actions promoting linkages between protected areas should be pursued. Identifying potential areas for assisted re-establishment via translocation offers the potential to expand the range of this species and alleviate risk.

The effectiveness of protected areas in the conservation of species with changing geographical ranges

A cornerstone of conservation is the designation and management of protected areas (PAs): locations often under conservation management containing species of conservation concern, where some development and other detrimental influences are prevented or mitigated. However, the value of PAs for conserving biodiversity in the long term has been questioned given that species are changing their distributions in response to climatic change. There is a concern that PAs may become climatically unsuitable for those species that they were designated to protect, and may not be located appropriately to receive newly-colonizing species for which the climate is improving. In the present study, we analyze fine-scale distribution data from detailed resurveys of seven butterfly and 11 bird species in Great Britain aiming to examine any effect of PA designation in preventing extinctions and promoting colonizations. We found a positive effect of PA designation on species' persistence at trailing-edge warm range margins, although with a decreased magnitude at higher latitudes and altitudes. In addition, colonizations by range expanding species were more likely to occur on PAs even after altitude and latitude were taken into account. PAs will therefore remain an important strategy for conservation. The potential for PA management to mitigate the effects of climatic change for retracting species deserves further investigation.

Permian brachiopoda from China and Malaysia : palaeoecology, palaeobiogeography and extinctions

The systematics, palaeoecology, palaeobiogeography and patterns of faunal change of Permian brachiopods from Sichuan, China and Pahang, Malaysia were investigated. The brachiopods from Pahang were systematically described for the first time. Five new species and one new genus were found in Sichuan, and two extinction and five origination events were recognised.

Limited population structure, genetic drift and bottlenecks characterise an endangered bird species in a dynamic, fire-prone ecosystem

Fire is a major disturbance process in many ecosystems world-wide, resulting in spatially and temporally dynamic landscapes. For populations occupying such environments, fire-induced landscape change is likely to influence population processes, and genetic patterns and structure among populations. The Mallee Emu-wren Stipiturus mallee is an endangered passerine whose global distribution is confined to fire-prone, semi-arid mallee shrublands in south-eastern Australia. This species, with poor capacity for dispersal, has undergone a precipitous reduction in distribution and numbers in recent decades. We used genetic analyses of 11 length-variable, nuclear loci to examine population structure and processes within this species, across its global range. Populations of the Mallee Emu-wren exhibited a low to moderate level of genetic diversity, and evidence of bottlenecks and genetic drift. Bayesian clustering methods revealed weak genetic population structure across the species' range. The direct effects of large fires, together with associated changes in the spatial and temporal patterns of suitable habitat, have the potential to cause population bottlenecks, serial local extinctions and subsequent recolonisation, all of which may interact to erode and homogenise genetic diversity in this species. Movement among temporally and spatially shifting habitat, appears to maintain long-term genetic connectivity. A plausible explanation for the observed genetic patterns is that, following extensive fires, recolonisation exceeds in-situ survival as the primary driver of population recovery in this species. These findings suggest that dynamic, fire-dominated landscapes can drive genetic homogenisation of populations of species with low-mobility and specialised habitat that otherwise would be expected to show strongly structured populations. Such effects must be considered when formulating management actions to conserve species in fire-prone systems.

Protected species use of a coastal marine migratory corridor connecting marine protected areas

The establishment of protected corridors linking the breeding and foraging grounds of many migratory species remains deficient, particularly in the world's oceans. For example, Australia has recently established a network of Commonwealth Marine Reserves, supplementing existing State reserves, to protect a wide range of resident and migratory marine species; however, the routes used by mobile species to access these sites are often unknown. The flatback marine turtle (Natator depressus) is endemic to the continental shelf of Australia, yet information is not available about how this species uses the marine area. We used a geospatial approach to delineate a coastal corridor from 73 adult female flatback postnesting migratory tracks from four rookeries along the north-west coast of Australia. A core corridor of 1,150 km length and 30,800 km2 area was defined, of which 52 % fell within 11 reserves, leaving 48 % (of equivalent size to several Commonwealth Reserves) of the corridor outside of the reserve network. Despite limited data being available for other marine wildlife in this region, humpback whale migratory tracks overlapped with 96 % of the core corridor, while the tracks of three other species overlapped by 5-10 % (blue whales, olive ridley turtles, whale sharks). The overlap in the distribution ranges of at least 20 other marine vertebrates (dugong, cetaceans, marine turtles, sea snakes, crocodiles, sharks) with the corridor also imply potential use. In conclusion, this study provides valuable information towards proposing new locations requiring protection, as well as identifying high-priority network linkages between existing marine protected areas. © 2014 Springer-Verlag Berlin Heidelberg.

Persistence of a threatened species in a modified alpine resort environment: the broad-toothed rat

Habitat change due to resort development threatens rare and endemic fauna of alpine and subalpine regions. There is an urgent need to understand species persistence in such areas. The broad-toothed rat (Mastacomys fuscus) is a rare, specialist species found in alpine and subalpine regions of Australia. We conducted fecal pellet surveys in an alpine resort to determine the species' distribution and habitat requirements. Eight individuals were radiotracked to investigate movement patterns and habitat use. Fecal pellets were found in areas of dense vegetation cover up to 1 m above ground. Home ranges were small (1,488-6,106 m²) and encompassed managed indigenous vegetation on or beside ski runs. Five individuals regularly crossed a narrow (3-5 m) cleared track. Two adult males dispersed (including traversing a wide grassy ski run) up to 1 km. The ability to cross modified areas and move throughout the landscape is proposed as a key factor facilitating the persistence of M. fuscus in the resort. Enhancing the capacity of species to move between habitat patches should be incorporated into alpine resort management plans. Such management will become increasingly important as anthropogenic disturbance increases in alpine regions.

The Economics of Threatened Species Conservation: A Review and Analysis

Stabilizing human population size and reducing human-caused impacts on the environment are keys to conserving threatened species (TS). Earth's human population is ~ 7 billion and increasing by ~ 76 million per year. This equates to a human birth-death ratio of 2.35 annually. The 2007 Red List prepared by the International Union for Conservation of Nature and Natural Resources (IUCN) categorized 16,306 species of vertebrates, invertebrates, plants, and other organisms (e.g., lichens, algae) as TS. This is ~ 1 percent of the 1,589,161 species described by IUCN or ~ 0.0033 percent of the believed 5,000,000 total species. Of the IUCN’s described species, vertebrates comprised relatively the most TS listings within respective taxonomic categories (5,742 of 59,811), while invertebrates (2,108 of 1,203,175), plants (8,447 of 297,326), and other species (9 of 28,849) accounted for minor class percentages. Conservation economics comprises microeconomic and macroeconomic principles involving interactions among ecological, environmental, and natural resource economics. A sustainable-growth (steady-state) economy has been posited as instrumental to preserving biological diversity and slowing extinctions in the wild, but few nations endorse this approach. Expanding growth principles characterize most nations' economic policies. To date, statutory fine, captive breeding cost, contingent valuation analysis, hedonic pricing, and travel cost methods are used to value TS in economic research and models. Improved valuation methods of TS are needed for benefit-cost analysis (BCA) of conservation plans. This Chapter provides a review and analysis of: (1) the IUCN status of species, (2) economic principles inherent to sustainable versus growth economies, and (3) methodological issues which hinder effective BCAs of TS conservation.

Hybridization and Introgression Between Native and Alien Species

Human activities, such intentional and unintentional transplantations, and habitat alterations including the establishment of migration corridors, generate increasing opportunities for formerly allopatric taxa to meet and to hybridize. There is indeed increasing evidence that these introduced plant and animal taxa (including crop plants and domesticated animal taxa) frequently hybridize with native relatives and with other introduced taxa, leading to a growing concern that these hybridizations may compromise the genetic integrity of native taxa to the point of causing extinctions (Abbott 1992; Rhymer and Simberloff 1996; Levin et al. 1996; Ellstrand and Schierenbeck 2000; Vilà et al. 2000). A decade ago, Rhymer and Simberloff (1996) stated in their review on this topic that the known cases are probably just the tip of the iceberg.Using the search term ‘hybridization and introgression’, the Web of Science database yields a total of 1,178 research articles, of which 935 (or 80 %) have been published after 1995 (Fig. 16.1). Indeed, the evidence for natural and man-induced hybridization and introgression appears to have increased exponentially these last few years.

Species-level selection reduces selfishness through competitive exclusion

Adaptation does not necessarily lead to traits which are optimal for the population. This is because selection is often the strongest at the individual or gene level. The evolution of selfishness can lead to a 'tragedy of the commons', where traits such as aggression or social cheating reduce population size and may lead to extinction. This suggests that species-level selection will result whenever species differ in the incentive to be selfish. We explore this idea in a simple model that combines individual-level selection with ecology in two interacting species. Our model is not influenced by kin or trait-group selection. We find that individual selection in combination with competitive exclusion greatly increases the likelihood that selfish species go extinct. A simple example of this would be a vertebrate species that invests heavily into squabbles over breeding sites, which is then excluded by a species that invests more into direct reproduction. A multispecies simulation shows that these extinctions result in communities containing species that are much less selfish. Our results suggest that species-level selection and community dynamics play an important role in regulating the intensity of conflicts in natural populations.

Physiological advantages of dwarfing in surviving extinctions in high-CO2 oceans

Excessive CO2 in the present-day ocean-atmosphere system is causing ocean acidification, and is likely to cause a severe biodiversity decline in the future, mirroring effects in many past mass extinctions. Fossil records demonstrate that organisms surviving such events were often smaller than those before, a phenomenon called the Lilliput effect. Here, we show that two gastropod species adapted to acidified seawater at shallow-water CO2 seeps were smaller than those found in normal pH conditions and had higher mass-specific energy consumption but significantly lower whole-animal metabolic energy demand. These physiological changes allowed the animals to maintain calcification and to partially repair shell dissolution. These observations of the long-term chronic effects of increased CO2 levels forewarn of changes we can expect in marine ecosystems as CO2 emissions continue to rise unchecked, and support the hypothesis that ocean acidification contributed to past extinction events. The ability to adapt through dwarfing can confer physiological advantages as the rate of CO2 emissions continues to increase.

Benthic foraminifera extinctions in the Cenozoic record

In the late Pliocene-middle Pleistocene a group of 95 species of elongate, cylindrical, deep-sea (lower bathyal-abyssal) benthic foraminifera became extinct. This Extinction Group (Ext. Gp), belonging to three families (all the Stilostomellidae and Pleurostomellidae, some of the Nodosariidae), was a major component (20-70%) of deep-sea foraminiferal assemblages in the middle Cenozoic and subsequently declined in abundance and species richness before finally disappearing almost completely during the mid-Pleistocene Climatic Transition (MPT). So what caused these declines and extinction? In this study 127 Ext. Gp species are identified from eight Cenozoic bathyal and abyssal sequences in the North Atlantic and equatorial Pacific Oceans. Most species are long-ranging with 80% originating in the Eocene or earlier. The greatest abundance and diversity of the Ext. Gp was in the warm oceanic conditions of the middle Eocene-early Oligocene. The group was subjected to significant changes in the composition of the faunal dominants and slightly enhanced species turnover during and soon after the rapid Eocene-Oligocene cooling event. Declines in the relative abundance and flux of the Ext. Gp, together with enhanced species loss, occurred during middle-late Miocene cooling, particularly at abyssal sites. The overall number of Ext. Gp species present began declining earlier at mid abyssal depths (in middle Miocene) than at upper abyssal (in late Pliocene-early Pleistocene) and then lower bathyal depths (in MPT). By far the most significant Ext. Gp declines in abundance and species loss occurred during the more severe glacial stages of the late Pliocene-middle Pleistocene. Clearly, the decline and extinction of this group of deep-sea foraminifera was related to the function of their specialized apertures and the stepwise cooling of global climate and deep water. We infer that the apertural modifications may be related to the method of food collection or processing, and that the extinctions may have resulted from the decline or loss of their specific phytoplankton or prokaryote food source, that was more directly impacted than the foraminifera by the cooling temperatures.

Morphology of Orbulina universa and Globorotalia scitula across local extinctions during Sapropel S5 (Eastern Mediterranean Sea, c.126-121 ka)

Extinction is a remarkably difficult phenomenon to study under natural conditions. This is because the outcome of stress exposure and associated fitness reduction is not known until the extinction occurs and it remains unclear whether there is any phenotypic reaction of the exposed population that can be used to predict its fate. Here we take advantage of the fossil record, where the ecological outcome of stress exposure is known. Specifically, we analyze shell morphology of planktonic Foraminifera in sediment samples from the Mediterranean, during an interval preceding local extinctions. In two species representing different plankton habitats, we observe shifts in trait state and decrease in variance in association with non-terminal stress, indicating stabilizing selection. At terminal stress levels, immediately before extinction, we observe increased growth asymmetry and trait variance, indicating disruptive selection and bet-hedging. The pre-extinction populations of both species show a combination of trait states and trait variance distinct from all populations exposed to non-terminal levels of stress. This finding indicates that the phenotypic history of a population may allow the detection of threshold levels of stress, likely to lead to extinction. It is thus an alternative to population dynamics in studying and monitoring natural population ecology.