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The Ponto-Caspian region is an endemicity hotspot that harbours several crustacean radiations, among which amphipods are the most diverse. These poorly known species are severely threatened in their native range, while at the same time they are invading European inland waters with significant ecological consequences. A proper taxonomic knowledge of this fauna is paramount for its conservation within the native region and monitoring outside of it. Here, we assemble a DNA barcode reference library for nearly 60% of all known Ponto-Caspian amphipod species. We use several methods to define molecular operational taxonomic units (MOTUs), based on two mitochondrial markers (COI and 16S), and assess their congruence with current species-level taxonomy based on morphology. Depending on the method, we find that 54–69% of species had congruent morpho-molecular boundaries. The cases of incongruence resulted from lumping distinct morphospecies into a single MOTU (7–27%), splitting a morphospecies into several MOTUs (4–28%), or both (4–11%). MOTUs defined by distance-based methods without a priori divergence thresholds showed the highest congruence with morphological taxonomy. These results indicate that DNA barcoding is valuable for clarifying the diversity of Ponto-Caspian amphipods, but reveals that extensive work is needed to resolve taxonomic uncertainties. Our study advances the DNA barcode reference library for the European aquatic biota, paving the way towards improved taxonomic knowledge needed to enhance monitoring and conservation efforts.

Non‐native species can be introduced to novel environments such as cities via wildlife trade. These populations may have conservation value—particularly if they are of a species threatened in its native range. Genetic tools can help assess the fitness of introduced populations by indicating if they are (1) suffering the consequences typically associated with small, isolated populations derived from few founders (e.g., inbreeding, low genetic diversity) or (2) they demonstrate gene flow indicative of mixed‐origin founders, successful breeding, and/or continual introductions of conspecifics. Such data can inform management interventions in the ex‐situ environment and highlight potential contributions of introduced populations to native‐range conservation. We examined multiple metrics of genetic health of a non‐native population of ca. 200 critically endangered Yellow‐crested Cockatoos (Cacatua sulphurea)—native to the eastern Indonesian archipelago—introduced to Hong Kong (HK) from the 1960s. We sequenced whole genomes and mitochondrial DNA of HK cockatoos and compared them to native‐range C. sulphurea, Sulphur‐crested Cockatoos (C. galerita) from Australia, and representatives from five additional wild parrot populations. Results indicate HK's cockatoos may have as yet evaded the severe negative genetic consequences of small, isolated populations, and currently have Ne and nucleotide diversity comparable to other wild parrot populations. Their genetic characteristics conform to those of young, mixed‐origin, non‐native populations: high individual‐level variance in relatedness and inbreeding/outbreeding, and influences of admixture. Given that C. sulphurea subspecies exhibit very low genetic distances, HK's city cockatoos are worthy of further examination as a potential genetic reservoir and rescue source for C. sulphurea.

Background The Lake Victoria basin is one of the most persistent hotspots of schistosomiasis in Africa, the intestinal form of the disease being studied more often than the urogenital form. Most schistosomiasis studies have been directed to Schistosoma mansoni and their corresponding intermediate snail hosts of the genus Biomphalaria , while neglecting S. haematobium and their intermediate snail hosts of the genus Bulinus . In the present study, we used DNA sequences from part of the cytochrome c oxidase subunit 1 ( cox 1) gene and the internal transcribed spacer 2 (ITS2) region to investigate Bulinus populations obtained from a longitudinal survey in Lake Victoria and neighbouring systems during 2010–2019. Methods Sequences were obtained to (i) determine specimen identities, diversity and phylogenetic positions, (ii) reconstruct phylogeographical affinities, and (iii) determine the population structure to discuss the results and their implications for the transmission and epidemiology of urogenital schistosomiasis in Lake Victoria. Results Phylogenies, species delimitation methods (SDMs) and statistical parsimony networks revealed the presence of two main groups of Bulinus species occurring in Lake Victoria; B. truncatus / B. tropicus complex with three species ( B. truncatus , B. tropicus and Bulinus sp. 1), dominating the lake proper, and a B. africanus group, prevalent in banks and marshes. Although a total of 47 cox 1 haplotypes, were detected within and outside Lake Victoria, there was limited haplotype sharing (only Haplotype 6 was shared between populations from Lake Victoria open waters and neighbouring aquatic systems) – an indication that haplotypes are specific to habitats. Conclusions The Bulinus fauna of Lake Victoria consists of at least B. truncatus , B. tropicus , Bulinus sp. 1 ( B. trigonus ?) and B. ugandae . The occurrence and wide distribution of Bulinus species in Lake Victoria potentially implies the occurrence of urogenital schistosomiasis in communities living along the shores and on islands of the lake who depend solely on the lake for their livelihood. More in-depth studies are needed to obtain a better picture of the extent of the disease in the Lake Victoria basin.

The unique aquatic Pontocaspian (PC) biota of the Black Sea Basin (BSB) is in decline. The lack of detailed knowledge on the status and trends of species, populations, and communities hampers a thorough risk assessment and precludes effective conservation. This paper reviews PC biodiversity trends in the BSB (Bulgaria, Romania, Moldova, Ukraine, and Russia) using endemic mollusks as a model group. We aim to assess changes in PC habitats, community structure, and species distribution over the past century and to identify direct anthropogenic threats. The presence/absence data of target mollusk species were assembled from literature, reports, and personal observations. Pontocaspian biodiversity trends in the northwestern BSB coastal regions were established by comparing 20th‐ and 21st‐century occurrences. The direct drivers of habitat and biodiversity change were identified and documented. We found that a pronounced decline of PC species and communities is driven by (a) damming of rivers, (b) habitat modifications that disturbed previous natural salinity gradients and settings in the studied area, (c) pollution and eutrophication, (d) invasive alien species, and (e) climate change. Four out of the 10 studied regions, namely, the Danube Delta–Razim Lake system, Dniester Liman, Dnieper–Bug estuary, and Taganrog Bay–Don Delta, contain favorable ecological conditions for PC communities and still host threatened endemic PC mollusk species. Distribution data are incomplete, but the scale of deterioration of PC species and communities is evident from the assembled data, as are major direct threats. Pontocaspian biodiversity in the BSB is profoundly affected by human activities. Standardized observation and collection data as well as precise definition of PC biota and habitats are necessary for targeted conservation actions. This study will help to set the research and policy agenda required to improve data collection to accommodate effective conservation of the unique PC biota. Distribution data of unique, endemic Pontocaspian (PC) biodiversity of the Black Sea Basin is incomplete, but the scale of deterioration of PC species and communities is evident from the assembled data, as are major direct threats. This review will help to set the research and policy agenda required to improve data collection to accommodate effective conservation of the unique PC biota.

Abstract Mutation rate is a fundamental parameter in population genetics. Apart from being an important scaling parameter for demographic and phylogenetic inference, it allows one to understand at what rate new genetic diversity is generated and what the expected level of genetic diversity is in a population at equilibrium. However, except for well-established model organisms, accurate estimates of de novo mutation rates are available for a very limited number of organisms from the wild. We estimated mutation rates (µ) in two marine populations of the nine-spined stickleback (Pungitius pungitius) with the aid of several 2- and 3-generational family pedigrees, deep (>50×) whole-genome resequences and a high-quality reference genome. After stringent filtering, we discovered 308 germline mutations in 106 offspring translating to µ = 4.83 × 10−9 and µ = 4.29 × 10−9 per base per generation in the two populations, respectively. Up to 20% of the mutations were shared by full-sibs showing that the level of parental mosaicism was relatively high. Since the estimated µ was 3.1 times smaller than the commonly used substitution rate, recalibration with µ led to substantial increase in estimated divergence times between different stickleback species. Our estimates of the de novo mutation rate should provide a useful resource for research focused on fish population genetics and that of sticklebacks in particular.

Abstract Many highly recognizable species lack genetic data important for conservation due to neglect over their hyperabundance. This likely applies to the Sulfur-crested Cockatoo (Cacatua galerita), one of the world's most iconic parrots. The species is native to Australia, New Guinea, and some surrounding Melanesian islands of the latter. Four subspecies are currently recognised based on morphology. Australian subspecies and populations are abundant, but several factors threaten those in New Guinea and Melanesia. Genetic data from natural populations are scarce—information that is vital to identifying evolutionarily significant units (ESUs) important for modern conservation planning. We used whole-genome resequencing to investigate patterns of differentiation, evolutionary affinities, and demographic history across C. galerita's distribution range to assess whether currently recognised subspecies represent ESUs. We complement this with an assessment of bioacoustic variation across the species' distribution landscape. Our results point to C. galerita sensu lato (s.l.) comprising two species. We restrict C. galerita sensu stricto (s.s.) to populations in Australia and the Trans-Fly ecodomain of southern New Guinea. The second species, recognised here as Cacatua triton, likely occurs over much of the rest of New Guinea. Restricting further discussion of intraspecific diversity in C. triton, we show that within C. galerita s.s. two ESUs exist, which align to Cacatua galerita galerita in eastern Australia and southern New Guinea and Cacatua galerita fitzroyi in northern and north-western Australia. We suggest that the evolution of these species and ESUs are linked to Middle and Late Pleistocene glacial cycles and their effects on sea level and preferential habitats. We argue that conservation assessments need updating, protection of preferential forest and woodland habitats are important and reintroductions require careful management to avoid possible negative hybridization effects of non-complementary lineages.

Aim It is predicted that the dispersal and gene flow of ectoparasites with wide host ranges are correlated with the vagilities of their most mobile hosts. To test this, the phylogeographical structure of a widespread generalist tick occurring on large ungulates was determined and compared with previously published host patterns. Location Africa. Methods mtDNA cytochrome c oxidase subunit I (COI) sequences were generated for 182 Hyalomma truncation specimens sampled from 21 Afro tropical localities. A subsample of these was sequenced for the nuclear Historie 3 (H3) and Calreticulin (CRT) regions. Phylogeographical inferences were made by using haplotype networks, a Bayesian analysis of population structure, isolation by distance (IBD) and a Bayesian gene tree. Demographic changes in the populations were determined with Bayesian skyline plots. Results Two highly divergent geographically confined mtDNA clades were detected, and these were partly supported by significant differentiation at nuclear DNA level. The clades differ by 9.88% (± 0.40%) mtDNA COI sequence divergence. The southern African clade, which expanded approximately 100 ka, shows no geographical barriers to dispersal and also no IBD. The northern African clade shows signs of IBD, at least five distinct genetic subgroups and an earlier expansion at 200 ka. Conclusion The phylogeography of the generalist tick is broadly congruent with host vicariance and supports the previously defined African Pleistocene savanna refugia. The magnitude of the sequence divergence between geographically separated genetic lineages suggests that H. truncatum comprises two distinct yet undescribed species. The dispersal of ectoparasites with wide host ranges is dependent on the ability of the various life stages of the parasite to survive in the off-host environment coupled to host movement.

Aim Elevated biodiversity is the result of the cradle, museum or sink functions. The contributions of these three functions to species accumulation and their changes through time remain unknown for glacial refugia. Additionally, our understanding of the role these functions played during pre‐glacial periods is limited. We test for changes in contributions of functions through time leading to the current diversity patterns using a model refugium and taxon. Location Anatolia, Western Palaearctic. Taxon Freshwater neritid snails (genus Theodoxus). Methods Assessments were made to define molecular operational taxonomic units (MOTUs) for Theodoxus and reaffirm the genus as a suitable model taxon with elevated interspecific diversity in noted glacial refugia. Thereafter, we constructed a time‐calibrated multilocus Bayesian phylogeny of mtDNA and nDNA by using both fossil data and published substitution rates. Ancestral area estimation was performed on the phylogeny to define the contribution of the functions through time. Results Accumulation of Theodoxus diversity in Anatolia over the Miocene–Pliocene transition is attributed to the museum function, but its contribution was small as only few divergence events occurred. The cradle function dominated during the Pliocene and Early Pleistocene, when most interspecific diversity built up and extant lineages in Anatolia were established. The sink function acted from the Middle Pleistocene to present‐day, but with only a small contribution to the total extant Anatolian interspecific diversity. Main conclusion Our results do not entirely mitigate the role glacial cycles played in species accumulation, but highlight Ice Ages may have been less effective in forcing temperate aquatic interspecific diversity into more opportune areas. The elevated diversity in refugia may rather be the result of earlier in situ diversification. Elevated interspecific diversity attributed to the legacy of glacially forced retreats may need to be re‐evaluated in cases where refugia have long and complex geological histories such as Anatolia. These results highlight the importance of considering species accumulation through a temporal perspective to adequately explain present‐day biodiversity patterns.

Defining and recording the loss of species diversity is a daunting task, especially if identities of species under threat are not fully resolved. An example is the Pontocaspian biota. The mostly endemic invertebrate faunas that evolved in the Black Sea – Caspian Sea – Aral Sea region and live under variable salinity conditions are undergoing strong change, yet within several groups species boundaries are not well established. Collection efforts in the past decade have failed to produce living material of various species groups whose taxonomic status is unclear. This lack of data precludes an integrated taxonomic assessment to clarify species identities and estimate species richness of Pontocaspian biota combining morphological, ecological, genetic, and distribution data. In this paper, we present an expert-working list of Pontocaspian and invasive mollusc species associated to Pontocaspian habitats. This list is based on published and unpublished data on morphology, ecology, anatomy, and molecular biology. It allows us to (1) document Pontocaspian mollusc species, (2) make species richness estimates, and (3) identify and discuss taxonomic uncertainties. The endemic Pontocaspian mollusc species richness is estimated between 55 and 99 species, but there are several groups that may harbour cryptic species. Even though the conservation status of most of the species is not assessed or data deficient, our observations point to deterioration for many of the Pontocaspian species.

To date, limited research has taken place on the evolutionary history of biodiversity in the high-altitude zones of southern Africa, particularly the Lesotho Highlands. The few studies that do exist point to similar high-altitude zones being either prolific museums (i.e., refugia and cradles) for cold-evolved species or sinks for temperate species post the Last Glacial Maximum, yet the role this zone has played for freshwater biodiversity is unknown for almost all freshwater taxa. In this study, we address this lack of knowledge by looking at the phylogeography of the freshwater limpet genus, Burnupia , across its southern and eastern African range, but particularly focusing on the Lesotho Highlands. We used COI data to reconstruct the evolutionary history of the genus, quantify phylogenetic species diversity, test both isolation by distance (IBD) and by elevation (IBE) and model ancestral area estimation “in” and “out” of the Highlands to determine: 1) The diversity and endemicity of Burnupia spp. in the Highlands in comparison to the broader southern African region and 2) when did the colonisation of the Highlands happen. Our results showed that at least two of the nine southern African phylogenetic species delimited occur in the Highlands (which appears average for the geographical extent of this area in comparison to the broader southern African region) and that the genus has been present in the Lesotho Highlands for somewhere between 1.38–0.23 million years. However, we found the endemicity of at least one of the two Highland species, supported by weak but significant IBD and IBE in Burnupia . Therefore we favour the notion that the Highlands are likely an important haven for cold-evolved species. As our results also generated a lot of data useful for Burnupia systematics, we discuss some taxonomic implications of our findings.