Manuel Lopes-Lima

Manuel Lopes-Lima
University of Porto | UP · Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO)

PhD

About

246
Publications
127,428
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Introduction
Manuel Lopes-Lima is a researcher at CIBIO/InBIO - Research Centre and the current (IUCN/SSC) Coordinator of the Red List Authority on Freshwater Bivalves within the Molluscs Specialist Group. His research interests are related with the global conservation of freshwater mussels including evolution, phylogeny, phylogeography, genetic diversity and ecophysiology. He is also an active promoter of international research efforts around this faunistic group.
Additional affiliations
February 2016 - August 2018
University of Porto
Position
  • Research Associate
January 2015 - January 2016
University of Porto
Position
  • Research Associate
January 2009 - January 2014
University of Porto
Position
  • Research Associate

Publications

Publications (246)
Article
In Europe, a total of 20 freshwater mussel species are currently considered valid, of which 13 (65%) are classified as threatened or near threatened on the International Union for the Conservation of Nature (IUCN) Red List of species. Given their precarious conservation status there is a pressing need to provide a roadmap for the conservation of th...
Article
Full-text available
Genomic tools applied to non-model organisms are critical to design successful conservation strategies of particularly threatened groups. Freshwater mussels of the Unionida order are among the most vulnerable taxa and yet almost no genetic resources are available. Here, we present the gill transcriptomes of five European freshwater mussels with hig...
Article
Chamberlainia hainesiana (Lea, 1856) (Unionidae) is the most economically important freshwater mussel in Thailand and is commonly used in food, spiritual ceremonies and pearl culture. Despite the clear economic importance of this monotypic genus, the distribution and diversity of Chamberlainia Simpson, 1900 are poorly understood. We set out to re-e...
Article
Full-text available
Traditional detection of aquatic invasive species via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindran...
Article
Full-text available
1. Freshwater mussels (Mollusca: Bivalvia: Unionida) have a broad global distribution on every continent except Antarctica. However, due to human activities, the diversity of freshwater mussels is seriously globally threatened. China is an important global biodiversity hotspot for this fauna. 2. Here, we comprehensively review the 99 currently reco...
Article
The freshwater pearl mussel Margaritifera margaritifera has been suffering major population declines in Europe. This endangered species is a host specialist and exclusively requires salmonid species (Salmo trutta and Salmo salar) to complete its life cycle. In theory, obligatory biotic interactions should deserve special conservation attention, bec...
Article
Full-text available
The naiads, large freshwater mussels (Unionida), have very long life spans, are large-bodied, and produce thousands to millions of larvae (glochidia) which typically must attach to host fish tissues to metamorphose into a juvenile mussel. Glochidia develop within a female's marsupial gill demibranch, thus their number is restricted by female size....
Article
1. Pseudunio marocanus (Pallary, 1918) is an endemic species of Morocco and is considered one of the world's 100 most threatened species. The life cycle of this critically endangered freshwater mussel remains unknown. However, knowledge about the discharge period of its larvae and its ecological fish hosts is crucial to adopt more effective conserv...
Article
Full-text available
The native freshwater bivalve fauna of Iraq (Unionidae) is comprised of five native species documented in the literature. Here we report the first occurrence of the widely introduced Sinanodonta woodiana and suggest it represents the temperate lineage of this species. This species has already reached a high population density where it was collected...
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• Most of the Bornean endemic freshwater mussel (Unionida) species known to date have not been recorded by science for the past 50 years or more, owing to a lack of research effort and presumed population losses. • This study assessed current patterns and recent changes in the diversity and distribution of freshwater mussels in north-eastern Borneo...
Article
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Theidentification of key biodiversity areas (KBA) was initiated by the International Union for Conservation of Nature in 2004 to overcome taxonomic biases in the selection of important areas for conservation, including freshwater ecosystems. Since then, several KBAs have been identified mainly based on the presence of trigger species (i.e., species...
Article
Full-text available
Located at the junction between Europe, Africa, and Asia, with distinct evolutionary origins and varied ecological and geographical settings, together with a marked history of changes in orogeny and configuration of the main river basins, turned the Eastern Mediterranean into a region of high diversity and endemism of freshwater taxa. Freshwater m...
Article
Full-text available
Located at the junction between Europe, Africa, and Asia, with distinct evolutionary origins and varied ecological and geographical settings, together with a marked history of changes in orogeny and configuration of the main river basins, turned the Eastern Mediterranean into a region of high diversity and endemism of freshwater taxa. Freshwater mu...
Article
Full-text available
Droughts can change the distribution and alter the behaviour, phenology and physiology of many species, leading in extreme cases to high mortalities or even extirpation. In this study, a before/after comparison was performed in two Portuguese river basins (Rabaçal and Tuela) to assess the possible effects of an extreme drought on the abundance and...
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Full-text available
South-western Australia is isolated from other forested regions of Australia by desert and bounded on southern and western sides by the Southern and Indian Oceans, respectively, with Westralunio carteri (Iredale, 1934) as the sole endemic freshwater mussel. Its conservation status is vulnerable. This species has a history of nomenclatural change an...
Article
Full-text available
Freshwater ecosystems are the most vulnerable worldwide and freshwater bivalves rank amongst the most threatened animals in the world. Surveying and monitoring freshwater bivalves are difficult tasks: they are difficult to find, hard to identify (taxonomic expertise is needed), and working underwater is technically challenging. It is therefore cruc...
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With the biodiversity crisis continuing unchecked, we need to establish levels and drivers of extinction risk, and reassessments over time, to effectively allocate conservation resources and track progress towards global conservation targets. Given that threat appears particularly high in freshwaters, we assessed the extinction risk of 1428 randoml...
Article
Full-text available
Molluscs are among the most diverse and widespread animal groups in freshwater habitats. Unfortunately, like most freshwater taxa, they are decreasing dramatically and are now among the most threatened animals on Earth, with many species already extinct or on the brink of extinction. Here, we review our current knowledge on the biodiversity and con...
Article
• Freshwater mussels (Order Unionida) are highly threatened. Interspecific competition for food sources with invasive alien species is considered to be one of the factors responsible for their decline because successful invaders are expected to have wider trophic niches and more flexible feeding strategies than their native counterparts. • In this...
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Full-text available
A freshwater mussel in the genus Hyriopsis Conrad, 1853 is described from the Chao Phraya Basin in central Thailand as Hyriopsis panhai, new species. This new species was once included in Hyriopsis bialata Simpson, 1900, but morphological investigations and multi-locus phylogeny based on concatenated data of COI, 16S, and 28S genes retrieved it as...
Article
Full-text available
In this correspondence, we present a summary of taxonomic names of freshwater Mollusca introduced by Dr. Nguyen N. Thach, an enthusiastic and productive malacologist from Vietnam. We show that this researcher described one new genus and 12 new nominal species of freshwater molluscs from Southeast Asia. Two of these nominal species, Sinanodonta hung...
Article
The first animal mitochondrial genomes to be sequenced were of several vertebrates and model organisms, and the consistency of genomic features found has led to a ‘textbook description’. However, a more broad phylogenetic sampling of complete animal mitochondrial genomes has found many cases where these features do not exist, and the phylum Mollusc...
Article
Full-text available
Since historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially...
Article
Full-text available
In this study, we present an announcement of Novaya Zemlya Collared Lemming Dicrostonyx torquatus ungulatus (von Baer, 1841) complete mitogenome. This rodent was described historically as an Arctic Collared Lemming subspecies endemic to Novaya Zemlya (Arctic Russia) but its taxonomic status was unclear due to the lack of available molecular data. B...
Article
Anthropogenic freshwater habitats may provide undervalued prospects for long‐term conservation as part of species conservation planning. This fundamental, but overlooked, issue requires attention considering the pace that humans have been altering natural freshwater ecosystems and the accelerated levels of biodiversity decline in recent decades. We...
Article
Full-text available
The morphological plasticity of bivalve species may impair their correct identification. Pisidium species (Sphaeriidae) are difficult to distinguish, notably the common pea clam, Pisidium ca-sertanum (Poli, 1791), which is a polymorphic species, often misidentified and confused with other Pisidium species. This is especially true since this species...
Article
Captive breeding is an effective conservation strategy, but it has risks, especially when a life history stage of an organism is bypassed. Freshwater mussels (Unionida) are critically imperiled, and their larvae are parasites on fishes. Traditional mussel captive breeding involves artificially infesting fishes with larvae (in vivo), but increasingl...
Article
• Freshwater ecosystems are essential to human well‐being and most have high biodiversity. However, this biodiversity has been suffering severe declines owing to the expansion of human activities. Protected areas (PAs) are essential for biodiversity conservation and have proved to be successful in stopping species extirpation if managed properly. U...
Chapter
Although biodiversity is considered a value to be protected to avoid the degradation of ecosystem functions, conservation practices ignore the role of many species. Species are not protected according to their degree of risk, but according to their degree of attractiveness. The so-called iconic species are used as flag species to convince the publi...
Article
The Unionidae represent an excellent model taxon for unravelling the drivers of freshwater diversity, but, phylogeographic studies on Southeast Asian taxa are hampered by lack of a comprehensive phylogeny and mutation rates for this fauna. We present complete female- (F) and male-type (M) mitogenomes of four genera of the Southeast Asian clade Cont...
Article
Full-text available
Through the Habitats Directive (92/43/EEC) and the financial investments of the LIFE projects, Europe has become an experimental arena for biological conservation. With an estimated annual budget of €20 billion, the EU Biodiversity Strategy for 2030 has set an ambitious goal of classifying 30% of its land and sea territory as Protected Areas and en...
Preprint
Full-text available
Since historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially...
Article
Full-text available
Many landscape and biotic processes shape the genetic structure of populations. The genetic structure of species with parasitic stages may also depend on the life history and ecology of their host. We investigated population genetic structure of the mussel Margaritifera margaritifera in Southern Sweden, and in relation to the population size and li...
Article
Full-text available
The number of non-native freshwater fishes in the Iberian Peninsula has been greatly increasing. In this study, individuals of the genus Phoxinus were detected in 18 out of 138 stream sites sampled across the Douro Basin in 2017 and 2018. A total of 26 individuals were barcoded using partial cytochrome c oxidase subunit I (COI) and cytochrome b (cy...
Preprint
Full-text available
Through the Habitats Directive (92/43/EEC) and the LIFE projects financial investments, Europe has been the world experimental arena for biological conservation. With an estimated budget of 20 billion euro/year, the EU Biodiversity Strategy for 2030 has set an ambitious goal of reaching 30% Protected Areas and ensure no deterioration in conservatio...
Article
Full-text available
Freshwater mussels are a critically imperiled group of mollusks that play key ecological roles and provide important services to humans. The Ambleminae is the only subfamily of these mussels, endemic to North America. Complete mitogenomes have only been sequenced for two of five tribes of the subfamily. Pleurobema oviforme, Amblema plicata, and Pop...
Article
Freshwater bivalves are highly threatened and globally declining due to multiple anthropogenic impacts, making them important conservation targets. Because conservation policies and actions generally occur at the species level, accurate species identification and delimitation is critical. A recent phylogenetic study of Italian mussel populations re...
Preprint
Full-text available
Traditional detection of aquatic invasive species, via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindra...
Preprint
A protocol for the metabarcoding of DNA samples using nanopore technology, for the purposes of biomonitoring, biodiversity assessment, DNA-based diet analysis, or other related applications. The protocol is being used in our laboratory for detecting aquatic invasive bivalve species and for measuring biodiversity of fish and other vertebrates from w...
Article
Full-text available
This contribution presents the first record of the Asian clam Corbicula fluminea Müller, 1774 in Greece. The species was collected in Erythropotamos River (Reka Luda Луда река), one of the main tributaries of Evros River (classical name of the Maritsa river), thus being the southernmost record of this invasive bivalve in the Balkan Peninsula. The m...
Article
Full-text available
The freshwater mussel fauna of Borneo is highly endemic, with at least 11 species being unique to that island. Most of these species have not been recorded for at least 50 years owing to a lack of sampling effort and large-scale habitat destruction and degradation. Surveys conducted in 2016 across much of Malaysian Borneo failed to locate four out...
Data
Commented maps of all the freshwater bivalve species in France with distinction between traditional data and eDNA data
Article
Full-text available
1. The freshwater mussel (Unionida) fauna of the Yangtze River is among the most diverse on Earth. In recent decades, human activities have caused habitat degradation in the river, and previous studies estimated that up to 80% of the mussel species in the Yangtze River are Threatened or Near Threatened with extinction. However, a comprehensive and...
Preprint
A protocol for the metabarcoding of DNA samples using nanopore technology, for the purposes of biomonitoring, biodiversity assessment, DNA-based diet analysis, or other related applications. The protocol is being used in our laboratory for detecting aquatic invasive bivalve species and for measuring biodiversity of fish and other vertebrates from w...
Article
Full-text available
While a growing body of modern phylogenetic research reveals that the Western Indochina represents a separate biogeographic subregion having a largely endemic freshwater fauna, the boundaries of this subregion are still unclear. We use freshwater mussels (Unionidae) as a model to reconstruct spatial patterns of freshwater biogeographic divides thro...
Article
1. Coextinction is the simplest form of secondary extinction and freshwater mussels (Bivalvia, Unionida) may be particularly prone to this phenomenon as their life cycle includes an obligatory parasitic larval stage on fish hosts. 2. The main aims of this study were to determine the possible ecological fish hosts of Anodonta anatina (Linnaeus, 175...
Article
Full-text available
Mollusca is the second most species-rich phylum within the metazoans, displaying critical economic, ecological and scientific importance. Yet, they are still largely underrepresented with respect to genomic resources. The emergence of next-generation sequencing technologies has revolutionized deep-scale genomic characterization of non-model organis...
Article
Full-text available
The Yangtze River Basin (Changjiang Basin) hosts one of the most diverse freshwater mussel assemblages on Earth. However, due to human activities this fauna is dramatically imperiled in this region, highlighting the need for urgent conservation measures. To better protect and conserve these taxa, it is crucial to understand the main drivers that co...
Data
Supplementary Figure 1. Habitats of freshwater mussels (Unionidae) in European Russia and Siberia • Supplementary Figure 2. Habitats of freshwater mussels (Unionidae) in the Russian Far East and Pacific Ocean islands • Supplementary Figure 3. Scatter plot of principal component analysis (PCA) based on the presence-absence dataset on freshwater mu...
Article
Full-text available
Freshwater mussels are ecosystem engineers and keystone species in aquatic environments. Unfortunately, due to dramatic declines this fauna is among the most threatened globally. Here, we clarify the taxonomy and biogeography of Russian Unionidae species based on the most comprehensive multi-locus dataset sampled to date. We revise the distribution...