Evolutionarily Significant Units Research Articles

Population structure, genetic diversity and evolutionary history of the narrow endemic squirrel Sciurus meridionalis

Endemic species and their genetic diversity are critical components of global biodiversity, yet they usually face a higher risk of decline and extinction than species with broader distributions. Loss of genetic diversity within geographically restricted and fragmented ranges plays a significant role in driving endemic species to extinction, threatening their ability to adapt to environmental challenges. Hence, considering genetic diversity and its spatial distribution within populations is mandatory in planning conservation actions for narrow endemic species. Here, we investigated the population genetic diversity, structure and evolutionary history of the Calabrian black squirrel Sciurus meridionalis, a species endemic to the Calabrian region in the south of the Italian peninsula. A fine-scale sampling procedure was carried out throughout the whole species range, and genetic variation was assessed from multiple mitochondrial and nuclear markers. Phylogeographic and population structure analyses showed three evolutionary significant units within the current species range, each characterised by extremely low levels of genetic diversity. Bayesian phylogeographic analyses suggested that Calabrian black squirrel populations experienced a range fragmentation during the Last Glacial Maximum (∼20 ka), which geographically mirrors the three main mountain massifs within the species range. Historical demographic reconstructions revealed a recent and still ongoing demographic expansion for Calabrian black squirrel populations, likely promoted by a concurrent expansion of the Calabrian black pine in this area. Overall, our findings clarify the designation of the evolutionary significant units for a narrow endemic squirrel and underscore the importance of analysing range-wide population genetic data and considering species interactions when defining management strategies for narrow endemic species’ conservation.

Distinct taxonomic practices impact patterns of bird endemism in the South American Cerrado savannas

Abstract Identifying endemic species and the areas of endemism delimited by them is central to biogeography. However, the impact of distinct taxonomic approaches on these patterns is often neglected. We investigated how three different taxonomic approaches impact the patterns of bird endemism in the Cerrado. The first two approaches (at species and subspecies levels) were based on traditional taxonomy based on the biological species concept. The third approach was based on a revised alternative taxonomy that sought to identify evolutionarily significant units (ESUs). In this third approach, after identifying the endemic taxa using traditional taxonomy, we revised their validity, removing biologically meaningless entities. We then detected the areas of endemism delimited by these endemic taxa under the three taxonomic approaches. We found that traditional taxonomy at the species level underestimated bird endemism by ignoring some ESUs that were considered subspecies. In contrast, traditional taxonomy at the subspecies level overestimated bird endemism, leading to the recognition of spurious areas of endemism because several of the purported endemic subspecies were taxonomic artefacts. The revised taxonomy provided a more refined picture of patterns of avian endemism in the Cerrado, suggesting that the use of ESUs improves the results of biogeographical analysis.

Revisiting the conservation genetics of Pampas deer (Ozotoceros bezoarticus)

The Pampas deer (Ozotoceros bezoarticus) is a unique species of neotropical cervid, that inhabits a wide range of open habitats including grasslands, pampas, savannas, and cerrado (Brazil) from -5° to -41° S.  The reduction of the area encompassed by these habitats has been dramatically reduced to less than 2 % by human activities such as agriculture, urbanization, and poaching.  Three decades ago, we initiated a molecular genetic study of the Pampas deer based on representative samples from throughout their geographic range.  Our aim is to reevaluate the effect that habitat fragmentation has had on gene flow among eight wildlife Pampas deer populations and one from the captive breeding centre Estación de Cría de Fauna Autóctona (ECFA).  We examined DNA sequences from three mitochondrial markers: the control region (D-loop), Cytochrome b (Cytb), and Cytochrome Oxidase I (COI).  Furthermore, we compared the resolution of the different mitochondrial markers to elucidate the phylogenetic and phylogeographic patterns of the species to define Evolutionary Significant Units (ESU`s).  The amount of gene flow was correlated with geographic distance among groups and populations and was consistent with limited dispersal being the primary determinant of genetic differentiation between populations.  Our results showed that the D-loop was the most appropriate marker for defining Evolutionary Significant Units.  We found that the critically endangered Paraná population showed significant genetic distance from the others and revealed unique haplotypes with all the mitochondrial markers.  The molecular genetic results provide a mandate for habitat restoration and design a management plan to conserve these relictual populations.

Population structure and connectivity among coastal and freshwater Kelp Gull (Larus dominicanus) populations from Patagonia.

The genetic identification of evolutionary significant units and information on their connectivity can be used to design effective management and conservation plans for species of concern. Despite having high dispersal capacity, several seabird species show population structure due to both abiotic and biotic barriers to gene flow. The Kelp Gull is the most abundant species of gull in the southern hemisphere. In Argentina it reproduces in both marine and freshwater environments, with more than 100,000 breeding pairs following a metapopulation dynamic across 140 colonies in the Atlantic coast of Patagonia. However, little is known about the demography and connectivity of inland populations. We aim to provide information on the connectivity of the largest freshwater colonies (those from Nahuel Huapi Lake) with the closest Pacific and Atlantic populations to evaluate if these freshwater colonies are receiving immigrants from the larger coastal populations. We sampled three geographic regions (Nahuel Huapi Lake and the Atlantic and Pacific coasts) and employed a reduced-representation genomic approach to genotype individuals for single-nucleotide polymorphisms (SNPs). Using clustering and phylogenetic analyses we found three genetic groups, each corresponding to one of our sampled regions. Individuals from marine environments are more closely related to each other than to those from Nahuel Huapi Lake, indicating that the latter population constitutes the first freshwater Kelp Gull colony to be identified as an evolutionary significant unit in Patagonia.

Genetic distinctiveness of an endangered falcon: Implications for conservation in Europe.

In the Falconidae, the genus Falco comprises species of large birds of prey with wide distribution worldwide. However, the European lanner falcon Falco biarmicus feldeggii is rapidly heading for global extinction following a dramatic decline caused by anthropogenic interference. Conservation projects are currently underway with the main purpose of increasing its population size in the Mediterranean basin through captive breeding and release of birds into the wild. To support the projects, and strengthen the legitimacy of conservation efforts consistently with the Evolutionary Significant Unit concept, we explored the possibility of characterising the gene pool of the European lanner and reliably distinguishing it from other falcon taxa inhabiting the Mediterranean area, which show morphological and genetic similarities. To address the issue, we examined genetic variability at the nuclear level through the analysis of 12 neutral Short Tandem Repeat loci, and, for the first time in these taxa, two single-copy functional genes, coding for the brain-derived neurotrophic factor precursor and the oocyte maturation factor, respectively. The second exon of the major histocompatibility complex class II B gene was also investigated. Additionally, to frame our data with previously published data, we assess variation at the mitochondrial level by sequencing portions of the cytochrome b, 12S rRNA gene, and the control region. Our results showed that the European lanner is highly distinct from other falcon taxa, as revealed by nuclear, but not by mitochondrial DNA. We discuss our findings focusing on their implications for the preservation of this highly endangered European bird, and highlighted the critical role of genetic information in planning and monitoring concrete interventions.

Evolutionary significant units (ESUs) and functional conservation units (FCUs) in the Phengaris (Maculinea) nausithous populations of East-Central Europe

The aim of this study was to analyse the level and structure of genetic and morphometric variation in the East-Central European populations of Phengaris (Maculinea) nausithous. On the basis of the life cycle of the species, we expected a low level of variation within the populations coupled with a relatively high level of differentiation among them. We also assumed that the differentiation among the populations has a regional pattern. In order to confirm these assumptions, we collected population samples from two regions within the Carpathian Basin (western Transdanubia and Transylvania) and from a region east of the Carpathian Mountains (Bukovina). The level of enzyme polymorphism and the amount of morphometric variation were investigated in the sampled populations. As the western (Transdanubia) and the eastern populations (Transylvania plus Bukovina) were suggested to belong to different subspecies (Rákosy et al. in Nota Lepidopterol 33:31–37, 2010), our working hypothesis was that these two groups of populations belong to different evolutionary significant units (ESUs). The results of all genetic analyses (PCA, Bayesian-clustering analysis and especially the UPGMA dendrogram) confirmed our assumption. The level of differentiation was higher between the western and eastern populations resulting in two monophyletic lineages of Phengaris (Maculinea) nausithous in East-Central Europe. This result suggests that these lineages can be considered as two different ESUs.

Genomics-informed conservation units reveal spatial variation in climate vulnerability in a migratory bird.

Identifying genetic conservation units (CUs) in threatened species is critical for the preservation of adaptive capacity and evolutionary potential in the face of climate change. However, delineating CUs in highly mobile species remains a challenge due to high rates of gene flow and genetic signatures of isolation by distance. Even when CUs are delineated in highly mobile species, the CUs often lack key biological information about what populations have the most conservation need to guide management decisions. Here we implement a framework for CU identification in the Canada Warbler (Cardellina canadensis), a migratory bird species of conservation concern, and then integrate demographic modelling and genomic offset to guide conservation decisions. We find that patterns of whole genome genetic variation in this highly mobile species are primarily driven by putative adaptive variation. Identification of CUs across the breeding range revealed that Canada Warblers fall into two evolutionarily significant units (ESU), and three putative adaptive units (AUs) in the South, East, and Northwest. Quantification of genomic offset, a metric of genetic changes necessary to maintain current gene-environment relationships, revealed significant spatial variation in climate vulnerability, with the Northwestern AU being identified as the most vulnerable to future climate change. Alternatively, quantification of past population trends within each AU revealed the steepest population declines have occurred within the Eastern AU. Overall, we illustrate that genomics-informed CUs provide a strong foundation for identifying current and future regional threats that can be used to inform management strategies for a highly mobile species in a rapidly changing world.

Is it time for genetic reinforcement of French Iberian ibex populations?

An evolutionary significant unit of the Iberian ibex (Capra pyrenaica), the Pyrenean ibex or “bucardo” (Capra pyrenaica pyrenaica) became extinct in its natural range, the Pyrenees, at the beginning of the twentieth-first century. Several years later (2014–2021) more than 250 specimens (C. p. victoriae) coming from the same donor population from central Spain were released in four localities of the French Pyrenees. Despite an initial fast demographic increase, the genetic variability of these populations remains low. Moreover, it is expected that genetic variability continues to decline due to genetic drift and that inbreeding accumulates. Here we revise options for genetic rescue or reinforcement of these populations involving future release of animals from different extant Spanish populations, mainly those belonging to the subpecies C. p. hispanica. The future hybridization between both phenotypes or “subspecies” may occur anyways in the next years, since currently there is a natural expansion of C. P. hispanica populations from the southern Pyrenees (Spanish side).

Relevance of molecular systematics in insect pest management

Insects (Insecta, Arthropoda), undeniably represent the most triumphant group of living organisms, in terms of evolutionary achievement, existing on earth. With over one million described species, they account for more than 75 percent of all known species, and it is estimated that at least 4-5 million insect species still remain undiscovered and undescribed (Stork, 2018). They represent one of the largest components of biodiversity in the world, closely associated with human's wellbeing in different forms like pests, natural enemies, producers of economic products and facilitators of pollination. In contemporary times, despite notable progress in agricultural output and economic prosperity in many regions, the problem of food insecurity persists as a significant concern affecting substantial segments of the global population (Palli, 2022). To cater the food demand of the fast expanding global population, intensive agricultural practices like extensive use of chemical fertilizers and insecticides, greater tillage and irrigation, as well as heavy mechanization are followed. The result is frequent outbreak of phytophagous insect pests along with a rapid decline in the biodiversity of beneficial insects including natural enemies and pollinators. It is estimated that crop losses caused by insects are a major problem in both developed and developing countries, destroying 18 to 20 per cent of the annual crop production globally, having worth over US$ 470 billion (Srivastava and Chakravarty, 2021). Initially, when pesticides were used to control or prevent insect pest outbreaks, the chemicals were often applied as soon as a problem was perceived, without accurate identification of the insect's identity or discovery of why the problem had developed in the first place. This lack of understanding of the cause of outbreak meant that the same problem could reoccur. Sustainable pest management requires a more scientific approach. The first step in this direction is the correct identification of the insect species. Accurate species identification, whether of the pest or its associated natural enemy along with their biological systematic studies provide backbone information for the success of any integrated pest management programme (Chakravarty et al., 2022). Traditional systematics or taxonomy was primarily reliant on morphology-based taxon identification systems. However, the process of morphological identification poses significant challenges in numerous insect taxa, mostly attributable to the absence of dependable diagnostic traits or the presence of cryptic species complexes (Shashank et al., 2022). Moreover, due to a decrease in the number of proficient morpho-taxonomists, specifically those specializing in lesser-known insect groups, there is a need for alternate approaches to species identification. Presently, entomologists are leveraging a wide array of molecular techniques that were previously untapped, while also embracing novel technologies under the paradigm of a "technology-driven revolution" in the field of systematics (Srivastava et al., 2019). Molecular techniques present a highly advantageous strategy for the identification and classification of insects, offering distinct benefits when compared to traditional morphological methods. Over the past twenty years, DNA barcoding has emerged as a swift and dependable technique for the identification of species, thereby revitalizing the field of taxonomic study. It refers to the technique, where short fragment of the conserved mitochondrial cytochrome c oxidase subunit I (COI) gene, the “DNA barcode,” is sequenced from a taxonomically undesignated specimen and comparisons are made with the DNA sequence of species of known origin for establishing a species level identification (Hebert et al., 2003). This approach has been frequently employed in various studies focusing on insects (and other arthropods in general), leading to the identification of previously unknown or cryptic species. Additionally, it has helped identify species complexes and evolutionary significant units, thereby establishing a basis for further comprehensive integrative taxonomic research (Firake and Behere, 2021). DNA barcoding considerably facilitates the monitoring of invasive species, vectors, and economically important endangered and/or endemic arthropod species. Furthermore, the utilization of DNA metabarcoding in ecological and surveillance initiatives has become increasingly prevalent. This approach enables the rapid evaluation of biodiversity in certain geographical regions, as well as the study of arthropod biosystems and communities that would otherwise be inaccessible. In recent times, entomologists in India have efficiently identified various invasive insect pest species, such as the elephant beetle, tomato pinworm, rugose spiralling whitefly, coconut case caterpillar, fall armyworm, and cassava mealy bug, by incorporating molecular systematics either as the sole method or in conjunction with traditional taxonomical tools (Srivastava and Chakravarty, 2021). In addition, there have been endeavours to offer extensive data through molecular characterization and/or DNA barcoding of indigenous organisms that serve as natural enemies and pollinators within diverse agricultural systems of India (Srivastava et al., 2019). A good number of insect genomes, particularly the mitochondrial genome have also been wholly sequenced in the country, including both crop pests and beneficial insects (Firake and Behere, 2021). However, our nation renowned for its exceptional biodiversity, exhibits a mere 3.73% coverage of DNA barcodes for its documented insect species. Notably, the orders Lepidoptera and Hemiptera are the most extensively represented in this limited dataset (Shashank et al., 2022). Such a delay in developing DNA barcode reference libraries for insects will set us back in our efforts to effectively document and preserve our rich biodiversity. The introduction of molecular systematics has also precipitated a revolution in our understanding of intraspecific genetic diversity and population genetic structure of several key insect pest species of agricultural importance in the country, helpful to detect the changes they adapt to overcome hurdles of various selection pressures including insecticides (Chakravarty et al., 2020). A necessity for the development of effective and safe management techniques for a target pest is the acquisition of comprehensive knowledge pertaining to its population structure and dynamics. Despite the emergence of inconsistencies between morphological and molecular phylogenies, as well as conflicting results from different molecular research, the utilization of phylogenomic analysis has proved helpful in resolving numerous controversial connections within insects. Over the past decade, our working group has devoted its research efforts entirely to this particular issue. Based on the molecular characterization with RAPD markers (Deepa and Srivastava, 2011) and COI gene (Chakravarty et al., 2021), phenotyping of immature and adult stages (Chakravarty and Srivastava, 2020; Chakravarty et al., 2023b), and other biological traits (Chakravarty et al., 2019 and 2023a), existence of sub-specific level variations among Helicoverpa armigera populations from diverse agro-ecologies of India has been deciphered. Similar studies for Leucinodes orbonalis (Padwal et al., 2022), Spodoptera litura (Ganguly et al., 2023) and Maruca vitrata (Mahalle et al., 2022) revealed genetic homogeneity for these pest species in the country. Further, Mahalle et al. (2023) have also screened publically accessible expressed sequence tag resources to identify microsatellites and evaluate their suitability as DNA markers for investigating gene flow patterns among populations of M. vitrata from pigeonpea fields throughout India. Molecular systematics has also proven to be a valuable tool in the identification of convergent evolution phenomena, such as the emergence of eusocial behaviours and caste systems among Hymenoptera (Berens et al., 2015); comprehending predator-prey dynamics within trophic food web investigations (Novotny and Miller, 2014), as well as resolving challenges associated with limited specimen availability or local species populations (Deng et al., 2019). Nevertheless, it is important to note that relying solely on molecular analyses to determine the identity of a species or assess population diversity can be precarious. This is due to potential biases introduced by the improper utilization of neighbor-joining trees, fixed distance thresholds, bootstrap resampling, interpretation of the barcoding gap, as well as limitations associated with DNA barcode repositories such as the Barcode of Life Data Systems (BOLD) and the National Centre for Biotechnology Information (NCBI). For instance, in a study conducted by Kvist (2013), it was found that 42% of invasive insects were not included in the BOLD database. Furthermore, the outcomes of phylogenetic analyses can be affected by various factors, such as the occurrence of recent speciation events, the presence of paraphyly, inadequate taxonomy, interspecific hybridization, and the high prevalence of endosymbiotic bacteria like Wolbachia, that hinders the replication or detection of the target sequence from insect specimens during the polymerase chain reaction, as highlighted by Shashank et al. (2022). Therefore, it is recommended that molecular methodologies should be utilized in conjunction with, rather than in lieu of, morphological identification in order to achieve optimal outcomes (Chakravarty et al., 2023b). Last but not the least, a note of appreciation for the “Journal of Environmental Biology” is also appropriate at this juncture. We are pleased to share our research experience and expertise through this editorial in the aforementioned journal, with which we have been affiliated for several years in various roles such as author, reviewer, and editor. This open access journal is notable for its comparatively modest processing charges, which enable researchers to publish their original work at an affordable cost. The enduring anticipation for highly critical reviews has contributed to the continued prominence of this journal within the realm of environmental science and related disciplines. We appreciate the visions of late Professor R.C. Dalela and his dedicated team, who have worked tirelessly over the years to make this journal a valuable resource for the global environmental outlook, with the ultimate aim of promoting societal well-being. Currently, the responsibility of overseeing this journal rests with Dr. Divakar Dalela, the Executive Editor, and Dr. Sumati Gaumat, the Editor, together with their dedicated publication team. They are diligently working towards upholding the international standards of this esteemed journal. We extend our best wishes for the continued success of the journal in the years to come.

Genomic insights into isolation of the threatened Florida crested caracara (Caracara plancus).

We conducted a population genomic study of the crested caracara (Caracara plancus) using samples (n = 290) collected from individuals in Florida, Texas, and Arizona, United States. Crested caracaras are non-migratory raptors ranging from the southern tip of South America to the southern United States, including a federally protected relict population in Florida long thought to have been isolated since the last ice age. Our objectives were to evaluate genetic diversity and population structure of Florida's apparently isolated population and to evaluate taxonomic relationships of crested caracaras at the northern edge of their range. Using DNA purified from blood samples, we conducted double-digest restriction site associated DNA sequencing and sequenced the mitochondrial ND2 gene. Analyses of population structure using over 9,000 SNPs suggest that two major clusters are best supported, one cluster including only Florida individuals and the other cluster including Arizona and Texas individuals. Both SNPs and mitochondrial haplotypes reveal the Florida population to be highly differentiated genetically from Arizona and Texas populations, whereas, Arizona and Texas populations are moderately differentiated from each other. The Florida population's mitochondrial haplotypes form a separate monophyletic group, while Arizona and Texas populations share mitochondrial haplotypes. Results of this study provide substantial genetic evidence that Florida's crested caracaras have experienced long-term isolation from caracaras in Arizona and Texas and thus, represent a distinct evolutionary lineage possibly warranting distinction as an Evolutionarily Significant Unit (ESU) or subspecies. This study will inform conservation strategies focused on long-term survival of Florida's distinct, panmictic population.

Demographic history and conservation aspects of two relict shrubs (Daphnimorpha spp., Thymelaeaceae) showing disjunct and restricted distribution in the southern part of Japan

Climate relicts are of particular importance in evolutionary biology because of the strategies they may adopt for long-term survival despite climatic oscillations. However, because their current distribution is usually restricted and fragmented, many climatic relicts are at risk of extinction. Daphnimorpha (Thymelaeaceae) is a genus endemic to Japan that comprises two species (D. capitellata and D. kudoi) with a disjunct distribution in southern Japan. These two shrub species are endemic to a single mountain range. In this study, we conducted population genetic analyses using genome-wide single nucleotide polymorphisms obtained from multiplexed inter-simple sequence repeats genotyping by sequencing to reveal the phylogeographic history and obtain conservation implications for the two species. The results showed that these two species may have been isolated since the Tertiary period, supporting their status as climate relicts. In addition, D. kudoi showed clear genetic differentiation between the two mountains where it occurred (Mt. Nagata and Mt. Kuromi), with a decline in the effective population sizes inferred during the last glacial period. In contrast, D. capitellata showed no clear intraspecific genetic structure, and its effective population size was relatively stable. These differences could result in contrasting light tolerance between species. For conservation, we recommend managing these species as three evolutionarily significant units (ESUs): D. capitellata, D. kudoi population on Mt. Nagata, and D. kudoi population on Mt. Kuromi. Considering the limited gene flow among subpopulations and small population census, all ESUs require conservation attention to maintain or increase their effective population sizes.

Unveiling the Potential Distribution of the Highly Threatened Madeira Pipistrelle (Pipistrellus maderensis): Do Different Evolutionary Significant Units Exist?

The isolation of islands has played a significant role in shaping the unique evolutionary histories of many species of flora and fauna, including bats. One notable example is the Madeira pipistrelle (Pipistrellus maderensis), which inhabits the Macaronesian archipelagos of the Azores, Madeira, and the Canary Islands. Despite the high biogeographic and conservation importance of this species, there is limited information on its ecology and evolutionary history across different archipelagos. In our study, we employed species distribution models (SDMs) to identify suitable habitats for the Madeira pipistrelle and determine the environmental factors influencing its distribution. Additionally, we conducted molecular comparisons using mitochondrial DNA data from various Macaronesian islands. Molecular analyses provided compelling evidence for the presence of distinct Evolutionary Significant Units on the different archipelagos. We identified distinct haplotypes in the populations of Madeira and the Canary Islands, with a genetic distance ranging from a minimum of 2.4% to a maximum of 3.3% between samples from different archipelagos. In support of this, SDMs highlighted relevant dissimilarities between the environmental requirements of the populations of the three archipelagos, particularly the climatic niche. Our research demonstrates that deeper investigations that combine ecological, morphological, and genetic areas are necessary to implement tailored conservation strategies.

Strong Population Genetic Structure for the Endangered Micro-Trapdoor Spider Moggridgea rainbowi (Mygalomorphae, Migidae) in Unburnt Habitat after Catastrophic Bushfires

Catastrophic wildfires impacted large areas of western Kangaroo Island (KI), South Australia in 2019–2020, burning habitat for many species, including large proportions of the distributional range of the KI micro-trapdoor spider Moggridgea rainbowi, which led to it being listed as Endangered under Australia’s Environment Protection and Biodiversity Conservation Act (EPBC Act). In order to assess population genetic structure in M. rainbowi and detect diagnosable lineages and their distributional patterns across KI, 28 individuals were genotyped for 2495 loci, sampling from all known populations of the species. Population genetic and phylogenetic analyses of nuclear and mitochondrial sequence data provided strong support for three Evolutionarily Significant Units (ESUs) within M. rainbowi; two populations on eastern KI and a heavily fire-impacted western population. High levels of divergence and fixed allelic differences between 5 and 16% indicate a lack of gene flow between ESUs and long periods of isolation. Distributional patterns of these lineages match likely locations of isolation events caused by successive changes to sea level during the Quaternary (2.58 million years ago to present), which led to KI being intermittently connected to the mainland or separated into one or more islands. Our findings have strong conservation implications for M. rainbowi and highlight the importance of inclusion of population genetic structure to inform conservation strategies and to conserve lineage biodiversity at the species level and below.

A Synthesis of the Ecology and Conservation of Pseudoplatystoma Catfishes in the Neotropics

Species of the genus Pseudoplatystoma, the long-whiskered catfishes, are important in commercial and recreational fisheries in South America, and some species have become key to regional aquaculture. Some species of the genus are under pressure due to overfishing and the negative impacts of dams. Six questions are asked in this review: (i) What species are in the genus, and where are they distributed? (ii) What are the life histories and ecologies of Pseudoplatystoma species? (iii) What are the patterns of somatic growth for these species? (iv) What is known about the biomass, production, and population dynamics of Pseudoplatystoma? (v) What is the geographic distribution of genetic variation within Pseudoplatystoma species? (vi) What are the threats to the conservation of these species? The taxonomy of the genus currently includes eight species, respectively, distributed over the Orinoco, Amazon, Paraná, and São Francisco basins. Pseudoplatystoma catfishes typically exhibit longitudinal migrations for reproduction and lateral migration for feeding, but these patterns may vary among populations. The size of the first maturation of these catfishes varies between 57 cm to 82 cm in total length. Five of the eight species spawn during the rising water season. Pseudoplatystoma species can grow to about 130 cm in total length and 100 Kg in weight and live until 30 years of age, depending upon the species. Biomass production and population dynamics of these catfishes have not yet been fully described. Their life-history characteristics indicate that they are periodic strategists with associated population recruitment dynamics. Population genetic patterning varies among Pseudoplatystoma species, with some degree of homing behavior and genetic differentiation among populations, indicating the need for management by applying the Management Unit and perhaps Evolutionary Significant Unit concepts. The main threats to the persistence of these catfishes are overfishing and alterations in and obstruction of river flow due to the construction of hydropower dams. After synthesizing existing information on species of the genus Pseudoplatystoma, we offer suggestions for future research to fill critical gaps in the knowledge of this group.

Genetic evidence of population subdivision among Masai giraffes separated by the Gregory Rift Valley in Tanzania.

The Masai giraffe has experienced a population decline from 70,000 to 35,000 in the past three decades and was declared an endangered subspecies by the IUCN in 2019. The remaining number of Masai giraffe are geographically separated by the steep cliffs of the Gregory Rift escarpments (GRE) in Tanzania and Kenya dividing them into two populations, one west and one east of the GRE. The cliffs of the GRE are formidable barriers to east-west dispersal and gene flow and the few remaining natural corridors through the GRE are occupied by human settlements. To assess the impact of the GRE on Masai giraffe gene flow, we examined whole genome sequences of nuclear and mitochondrial DNA (mtDNA) variation in populations located east (Tarangire ecosystem) and west (Serengeti ecosystem) of the GRE in northern Tanzania. Evidence from mtDNA variation, which measures female-mediated gene flow, suggests that females have not migrated across the GRE between populations in the Serengeti and Tarangire ecosystems in the past ~289,000 years. The analysis of nuclear DNA variation compared to mtDNA DNA variation suggests that male-mediated gene flow across the GRE has occurred more recently but stopped a few thousand years ago. Our findings show that Masai giraffes are split into two populations and fulfill the criteria for designation as distinct evolutionary significant units (ESUs), which we denote as western Masai giraffe and eastern Masai giraffe. While establishing giraffe dispersal corridors across the GRE is impractical, conservation efforts should be focused on maintaining connectivity among populations within each of these two populations. The importance of these efforts is heightened by our finding that the inbreeding coefficients are high in some of these Masai giraffe populations, which could result in inbreeding depression in the small and fragmented populations.

Defining Evolutionary Conservation Units in the Macedonian Crested Newt, Triturus macedonicus (Amphibia; Salamandridae), in a Biodiversity Hotspot

In this study, we used genetic approaches to assess the conservation status of a protected amphibian species, the Macedonian crested newt, Triturus macedonicus, in Northern Pindos National Park (Epirus, Greece). Mitochondrial DNA sequences and multilocus genotypes of individuals from 38 breeding sites were used to infer their phylogenetic position and to detect and measure genetic variation patterns, population genetic structure, and levels of gene flow. The examined individuals fell within two major clades of the Macedonian crested newt phylogeny, being geographically separated by the Aoos River valley and Vikos Gorge. Both groups constitute separate gene pools, bearing private haplotypes and alleles, and the groups were found to be highly differentiated in both their mitochondrial and microsatellite markers. Thus, they meet all of the criteria needed to be characterized as evolutionary significant units (ESUs) that deserve a separate conservation status. Within each ESU, the particularly high inter-population differentiation and low migration rates imply a lack of connectivity between breeding sites and local isolation in favorable habitats. Our results can inform future programs and actions towards the conservation and management of the Macedonian crested newt in the area.

Phylogeographic analysis revealed allopatric distribution pattern and biogeographic processes of the widespread pale chub Opsariichthys acutipinnis-evolans complex (Teleostei: Cyprinidae) in southeastern China

Understanding phylogeographic patterns of widespread species can provide insights into their speciation processes and guide the conservation and management measures. In the present study, Cyt b sequences were used to investigate the phylogeographic structure of the Opsariichthys acutipinnis-evolans complex in southeastern China. The gene tree revealed six major lineages (lineage A-F) which were distributed allopatrically, with lineage B distributed in the western part (middle Yangtze and Pearl River) and the other lineages in the eastern part (lower Yangtze and coastal waters of southeastern China). Dating of the lineage diversification revealed the early eastward-westward divergence separating lineage A, B, and C during the late Pliocene and early Pleistocene (3.00, 2.61, and 2.12 Ma, respectively), possibly due to the uplift of the Qinghai-Tibetan Plateau and subsequent orogenies in southeastern China. The following northward-southward diversification resulted in the separation of lineage D, E, and F in the early-middle Pleistocene (1.33 and 0.95 Ma), likely associated with the enhanced succession of glacial cycles during the Early-Middle Pleistocene transition. Although the genetic divergence of 0.017–0.070 among lineages indicated possible different species, morphological characters failed to separate them. Therefore, they were treated as a species complex. Given the distinct genetic divergence of the various lineages, they were suggested as different evolutionary significant units.

Conservation prioritisation through genomic reconstruction of demographic histories applied to two endangered suids in the Malay Archipelago

AbstractAimThe biodiversity of the Malay Archipelago is the product of the region's rich biogeographical history with periods of island connectivity and isolation during the Pleistocene glacial cycles. Here, the case of two endemic suid species, the Javan (Sus verrucosus) and Bawean (S. blouchi) warty pigs, was used to illustrate how biogeographic processes and recent anthropogenic pressures can shape demographic histories with significant implications for species conservation.LocationMalay Archipelago, with focus on Bawean and Java.MethodsWe employed genome‐wide single nucleotide polymorphisms from the Porcine SNP60 v2 BeadChip to assess interspecific genetic differentiation, to estimate divergence times and to perform demographic model selection.ResultsIn contrast to the hypothesis of recent divergence during the last glacial maximum, S. blouchi was found to have diverged from S. verrucosus at least 166 k years ago following a founder event. The contemporary S. blouchi population was characterised by a recent bottleneck that reduced the effective population size to less than 20. The genomic assessment supports the single species status of S. blouchi, as was previously proposed based on morphometrics. The demographic history of S. verrucosus showed evidence of secondary contact with the sympatric banded pig (S. scrofa vittatus) that colonised Java 70 k years ago.Main ConclusionsWhile the Javan and Bawean warty pigs have persisted throughout the Pleistocene climatic oscillations, contemporary pressures from human activities threaten their survival and immediate action should be taken to grant legal protection to both S. verrucosus and S. blouchi. This study highlighted the use of demographic history modelling using genomic data to identify evolutionary significant units and inform conservation.

A preliminary note on population structure in eastern South Pacific common bottlenose dolphins, Tursiops truncatus

Previous studies of eastern South Pacific common bottlenose dolphins, Tursiops truncatus, defined offshore and inshore ecotypes in Peru based on cranial and tooth morphology, documented the presence of a single resident inshore community (‘pod-R’) in central-north Chile, and confirmed the presence of offshore bottlenose dolphins off Chile. Here, mtDNA control region (331bp) was examined to evaluate genetic relationships between four geographic areas: inshore pod-R (n=8), Chilean offshore population (n=8), Peruvian inshore (n=3) and offshore (n=12) ecotypes. This is the first genetic analysis of T. truncatus in this ocean basin. Phylogenetic analysis grouped the three Peruvian specimens morphologically identified as inshore ecotype in an independent cluster, supported by 100% bootstrap value. The net genetic distance between Peruvian inshore and Peruvian offshore ecotypes was estimated at 2.9%, and even higher when compared with Chilean bottlenose dolphins. Morphological and mtDNA evidence combined argues for considering inshore and offshore ecotypes as evolutionary significant units, to be managed accordingly. Despite its inshore behavioural ecology, pod-R presented a high divergence from the Peruvian inshore ecotype and a relatively closer affinity with the Chilean offshore stock (3.41% and 0.87% net interpopulational distance, respectively). However, homogeneity tests showed significant genetic differences of pod-R with all other groups, including Chilean offshore. This, combined with a low nucleotide diversity (0.0069) and behavioural observations, suggest that pod-R may be reproductively isolated and active protection measures are recommended. Only one haplotype from a total of 21 was shared by Peruvian and Chilean offshore animals. Their net genetic distance was estimated at 0.024 and no significant differences were found in haplotype frequencies, suggesting a single, wide-ranging ‘Peru-Chile offshore stock’.

GENETIC DIVERSITY AND STRUCTURE OF THE WHITE-FRONTED PARROT (AMAZONA ALBIFRONS) IN MEXICO

In this study we assessed the genetic diversity and differentiation, and genealogical relationships in a group of individuals of A. albifrons distributed on the Pacific slope and in the Yucatan Peninsula, Mexico using mitochondrial DNA markers.Both range regions the species showed a high genetic diversity, suggesting population expansion from a small effective population size. Genealogical relationships revealed the presence of two genetic groups that have gone through different demographic events, one in the Yucatan Peninsula and the other in the Pacific slope. Considering that the individuals of the Yucatan Peninsula formed a genetic group exclusive to the region due to isolation events and a unique evolutionary history, we suggest its recognition as an evolutionarily significant unit (ESU). In addition, considering the presence of unique haplotypes in the localities of Sinaloa and Michoacan, we recommended that conservation plans focus on these regions.