... SPATIAL MODELLING OF FRESHWATER FISH IN SEMI-ARID RIVER SYSTEMS: A TOOL FOR CONSERVATION AF F... more ... SPATIAL MODELLING OF FRESHWATER FISH IN SEMI-ARID RIVER SYSTEMS: A TOOL FOR CONSERVATION AF FILIPE, a IG COWX b and MJ COLLARES-PEREIRA a * ...
Over the last decade, steady advancements have been made in the use of DNA-based methods for dete... more Over the last decade, steady advancements have been made in the use of DNA-based methods for detection of species in a wide range of ecosystems. This progress has culminated in molecular monitoring methods being employed for the detection of several species for enforceable management purposes of endangered, invasive, and illegally harvested species worldwide. However, the routine application of DNA-based methods to monitor whole communities (typically a metabarcoding approach) in order to assess the status of ecosystems continues to be limited. In aquatic ecosystems, the limited use is particularly true for macroinvertebrate communities. As part of the DNAqua-Net consortium, a structured discussion was initiated with the aim to identify potential molecular methods for freshwater macroinvertebrate community assessment and identify important knowledge gaps for their routine application. We focus on three complementary DNA sources that can be metabarcoded: 1) DNA from homogenised sampl...
The Science of the total environment, Jan 24, 2018
We present the most updated list of non-native freshwater fauna established in Portugal, includin... more We present the most updated list of non-native freshwater fauna established in Portugal, including the Azores and Madeira archipelagos. This list includes 67 species at national level but corresponds to 84 species records, of which 53 are in the mainland, 23 in the Azores and 8 in Madeira archipelagos. We also discuss the progression of the cumulative number of introductions since 1800 and identify the most probable vectors of introduction, main taxonomic groups and their regions of origin. Furthermore, we review the existing knowledge about ecological and economic impacts, invasion risk and potential distribution of invaders, under present and future climatic conditions, and the applied management actions, including the production of legislation. Along the 20th century the number of successful introductions increased at an approximate rate of two new species per decade until the beginning of 1970s. Since then, this rate increased to about 14 new species per decade. These introducti...
The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the... more The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potentia...
Controlling for imperfect detection is important for developing species distribution models (SDMs... more Controlling for imperfect detection is important for developing species distribution models (SDMs). Occupancy-detection models based on the time needed to detect a species can be used to address this problem, but this is hindered when times to detection are not known precisely. Here, we extend the time-to-detection model to deal with detections recorded in time intervals and illustrate the method using a case study on stream fish distribution modeling. We collected electrofishing samples of six fish species across a Mediterranean watershed in Northeast Portugal. Based on a Bayesian hierarchical framework, we modeled the probability of water presence in stream channels, and the probability of species occupancy conditional on water presence, in relation to environmental and spatial variables. We also modeled time-to-first detection conditional on occupancy in relation to local factors, using modified interval-censored exponential survival models. Posterior distributions of occupancy p...
Freshwater ecosystems and biodiversity are among the most threatened at global scale, but efforts... more Freshwater ecosystems and biodiversity are among the most threatened at global scale, but efforts for their conservation have been mostly peripheral to terrestrial conservation. For example, Natura 2000, the world's largest network of protected areas, fails to cover adequately the distribution of rare and endangered aquatic species, and lacks of appropriate spatial design to make conservation for freshwater biodiversity effective. Here, we develop a framework to identify a complementary set of priority areas and enhance the conservation opportunities of Natura 2000 for freshwater biodiversity, using the Iberian Peninsula as a case study. We use a systematic planning approach to identify a minimum set of additional areas that would help i) adequately represent all freshwater fish, amphibians and aquatic reptiles at three different target levels, ii) account for key ecological processes derived from riverscape connectivity, and iii) minimize the impact of threats, both within prot...
Aim The question of how much of the shared geographical distribution of biota is due to environme... more Aim The question of how much of the shared geographical distribution of biota is due to environmental vs. historical constraints remains unanswered. The aim of this paper is to disentangle the contribution of historical vs. contemporary factors to the distribution of freshwater fish species. In addition, it illustrates how quantifying the contribution of each type of factor improves the classification of biogeographical provinces. Location Iberian Peninsula, south-western Europe (c. 581,000 km2). Methods We used the most comprehensive data on native fish distributions for the Iberian Peninsula, compiled from Portuguese and Spanish sources on a 20-km grid-cell resolution. Overall, 58 species were analysed after being categorized into three groups according to their ability to disperse through saltwater: (1) species strictly intolerant of saltwater (primary species); (2) species partially tolerant of saltwater, making limited incursions into saltwaters (secondary species); and (3) sal...
... SPATIAL MODELLING OF FRESHWATER FISH IN SEMI-ARID RIVER SYSTEMS: A TOOL FOR CONSERVATION AF F... more ... SPATIAL MODELLING OF FRESHWATER FISH IN SEMI-ARID RIVER SYSTEMS: A TOOL FOR CONSERVATION AF FILIPE, a IG COWX b and MJ COLLARES-PEREIRA a * ...
Over the last decade, steady advancements have been made in the use of DNA-based methods for dete... more Over the last decade, steady advancements have been made in the use of DNA-based methods for detection of species in a wide range of ecosystems. This progress has culminated in molecular monitoring methods being employed for the detection of several species for enforceable management purposes of endangered, invasive, and illegally harvested species worldwide. However, the routine application of DNA-based methods to monitor whole communities (typically a metabarcoding approach) in order to assess the status of ecosystems continues to be limited. In aquatic ecosystems, the limited use is particularly true for macroinvertebrate communities. As part of the DNAqua-Net consortium, a structured discussion was initiated with the aim to identify potential molecular methods for freshwater macroinvertebrate community assessment and identify important knowledge gaps for their routine application. We focus on three complementary DNA sources that can be metabarcoded: 1) DNA from homogenised sampl...
The Science of the total environment, Jan 24, 2018
We present the most updated list of non-native freshwater fauna established in Portugal, includin... more We present the most updated list of non-native freshwater fauna established in Portugal, including the Azores and Madeira archipelagos. This list includes 67 species at national level but corresponds to 84 species records, of which 53 are in the mainland, 23 in the Azores and 8 in Madeira archipelagos. We also discuss the progression of the cumulative number of introductions since 1800 and identify the most probable vectors of introduction, main taxonomic groups and their regions of origin. Furthermore, we review the existing knowledge about ecological and economic impacts, invasion risk and potential distribution of invaders, under present and future climatic conditions, and the applied management actions, including the production of legislation. Along the 20th century the number of successful introductions increased at an approximate rate of two new species per decade until the beginning of 1970s. Since then, this rate increased to about 14 new species per decade. These introducti...
The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the... more The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potentia...
Controlling for imperfect detection is important for developing species distribution models (SDMs... more Controlling for imperfect detection is important for developing species distribution models (SDMs). Occupancy-detection models based on the time needed to detect a species can be used to address this problem, but this is hindered when times to detection are not known precisely. Here, we extend the time-to-detection model to deal with detections recorded in time intervals and illustrate the method using a case study on stream fish distribution modeling. We collected electrofishing samples of six fish species across a Mediterranean watershed in Northeast Portugal. Based on a Bayesian hierarchical framework, we modeled the probability of water presence in stream channels, and the probability of species occupancy conditional on water presence, in relation to environmental and spatial variables. We also modeled time-to-first detection conditional on occupancy in relation to local factors, using modified interval-censored exponential survival models. Posterior distributions of occupancy p...
Freshwater ecosystems and biodiversity are among the most threatened at global scale, but efforts... more Freshwater ecosystems and biodiversity are among the most threatened at global scale, but efforts for their conservation have been mostly peripheral to terrestrial conservation. For example, Natura 2000, the world's largest network of protected areas, fails to cover adequately the distribution of rare and endangered aquatic species, and lacks of appropriate spatial design to make conservation for freshwater biodiversity effective. Here, we develop a framework to identify a complementary set of priority areas and enhance the conservation opportunities of Natura 2000 for freshwater biodiversity, using the Iberian Peninsula as a case study. We use a systematic planning approach to identify a minimum set of additional areas that would help i) adequately represent all freshwater fish, amphibians and aquatic reptiles at three different target levels, ii) account for key ecological processes derived from riverscape connectivity, and iii) minimize the impact of threats, both within prot...
Aim The question of how much of the shared geographical distribution of biota is due to environme... more Aim The question of how much of the shared geographical distribution of biota is due to environmental vs. historical constraints remains unanswered. The aim of this paper is to disentangle the contribution of historical vs. contemporary factors to the distribution of freshwater fish species. In addition, it illustrates how quantifying the contribution of each type of factor improves the classification of biogeographical provinces. Location Iberian Peninsula, south-western Europe (c. 581,000 km2). Methods We used the most comprehensive data on native fish distributions for the Iberian Peninsula, compiled from Portuguese and Spanish sources on a 20-km grid-cell resolution. Overall, 58 species were analysed after being categorized into three groups according to their ability to disperse through saltwater: (1) species strictly intolerant of saltwater (primary species); (2) species partially tolerant of saltwater, making limited incursions into saltwaters (secondary species); and (3) sal...
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Papers by Ana Filipe