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Captive breeding programs benefit from genetic analyses that identify relatedness between individuals, assign parentage to offspring, and track levels of genetic diversity. Monitoring these parameters across breeding cycles is critical to the success of a captive breeding program as it allows conservation managers to iteratively evaluate and adjust program structure. However, in practice, genetic tracking of breeding outcomes is rarely conducted. Here, we examined the first three offspring cohorts (2017–2020) of the genetically informed captive breeding program for the Floreana Island Galapagos giant tortoise, Chelonoidis niger. This captive breeding program is unique as the Floreana tortoise has been extinct since the 1800s, but its genome persists, in part, in the form of living hybrids with the extant Volcano Wolf tortoise, C. becki. Breeding over the study period took place at the Galapagos National Park Directorate breeding facility in four corrals, each containing three females and two males. Using 17 microsatellite markers, we were able to assign parentage to 94 of the 98 offspring produced over the study period. We observe that despite the addition of more founders since the pilot breeding program, the effective population size remains low, and changes to the arrangements of breeding corrals may be necessary to encourage more equal reproductive output from the males. This study demonstrates the value of hybrids for species restoration and the importance of continually reassessing the outcomes of captive breeding.

The status of the Fernandina Island Galapagos giant tortoise (Chelonoidis phantasticus) has been a mystery, with the species known from a single specimen collected in 1906. The discovery in 2019 of a female tortoise living on the island provided the opportunity to determine if the species lives on. By sequencing the genomes of both individuals and comparing them to all living species of Galapagos giant tortoises, here we show that the two known Fernandina tortoises are from the same lineage and distinct from all others. The whole genome phylogeny groups the Fernandina individuals within a monophyletic group containing all species with a saddleback carapace morphology and one semi-saddleback species. This grouping of the saddleback species is contrary to mitochondrial DNA phylogenies, which place the saddleback species across several clades. These results imply the continued existence of lineage long considered extinct, with a current known population size of a single individual.

The Norway rat (Rattus norvegicus) is a key pest species globally and responsible for seasonal outbreaks of the zoonotic bacterial disease leptospirosis in the tropics. The city of Salvador, Brazil, has seen recent and dramatic increases in human population residing in slums, where conditions foster high rat density and increasing leptospirosis infection rates. Intervention campaigns have been used to drastically reduce rat numbers. In planning these interventions, it is important to define the eradication units ‐ the spatial scale at which rats constitute continuous populations and from where rats are likely recolonizing, post‐intervention. To provide this information, we applied spatial genetic analyses to 706 rats collected across Salvador and genotyped at 16 microsatellite loci. We performed spatially explicit analyses and estimated migration levels to identify distinct genetic units and landscape features associated with genetic divergence at different spatial scales, ranging from valleys within a slum community to city‐wide analyses. Clear genetic breaks exist between rats not only across Salvador but also between valleys of slums separated by

We investigate the genetic relationships between purported island species of Pteropus fruit bat (Megachiroptera) from the western Indian Ocean islands using mitochondrial DNA sequencing in order to infer the pattern of colonisation of this biogeographic region. Most significantly, our genetic data questions the current taxonomic assignment based on morphology of many of the island species and subspecies, suggesting instead that many of the western Indian Ocean islands harbour 'races' of P. giganteus from mainland India. Our results strongly argue against a single colonisation event from mainland Asia. Evidence is presented for three colonisation events; the first to the western-most extremity of their range (Comoros and Pemba Island), the second to Rodrigues Island; and a third giving rise to the remaining extant island taxa, the latter two events occurring relatively recently and rapidly.

The Norway rat, Rattus norvegicus, is one of the most important pest species globally and the main reservoir of leptospires causing human leptospirosis in the urban slums of tropical regions. Rodent control is a frequent strategy in those settings to prevent the disease but rapid growth from residual populations and immigration limit the long-term effectiveness of interventions. To characterize the breeding ecology of R. norvegicus and provide needed information for the level of genetic mixing, which can help identify inter-connected eradication units, we estimated the occurrence of multiple paternity, distances between mothers and sires, and inbreeding in rats from urban slum habitat in Salvador, Brazil. We genotyped 9 pregnant females, their 66 offspring, and 371 males at 16 microsatellite loci. Multiple paternity was observed in 22% (2/9) of the study litters. Of the 12 sires that contributed to the 9 litters, we identified 5 (42%) of those sires among our genotyped males. Related males were captured in close proximity to pregnant females (the mean inter-parent trapping distance per litter was 70 m, ±58 m SD). Levels of relatedness between mother-sire pairs were higher than expected and significantly higher than relatedness between all females and non-sire males. Our findings indicate multiple paternity is common, inbreeding is apparent, and that mother-sire dyads occur in close proximity within the study area. This information is relevant to improve the spatial definition of the eradication units that may enhance the effectiveness of rodent management programs aimed at preventing human leptospirosis. High levels of inbreeding may also be a sign that eradication efforts are successful.

The ctenophore Mnemiopsis leidyi is one of the most successful marine bioinvaders on record. Native to the Atlantic coast of the Americas, M. leidyi invaded the Black Sea, Caspian and Mediterranean Seas beginning the in late 1980s, followed by the North and Baltic Seas starting in 2006, with major concomitant alterations in pelagic ecology, including fishery collapses in some cases. Using extensive native range sampling (21 sites), along with 11 invasive sites in the Black, Caspian, Mediterranean, North and Baltic Seas, we examined M. leidyi worldwide phylogeographic patterns using data from mitochondrial cytochrome b (cytb) and six nuclear microsatellite loci. Cytb and microsatellite data sets showed different levels of genetic differentiation in the native range. Analyses of cytb data revealed considerable genetic differentiation, recovering three major clusters (northwestern Atlantic, Caribbean, and South America) and further divided northwestern Atlantic sampling sites into three groups, separated approximately at Cape Hatteras on the US Atlantic coast and at the Floridian peninsula, separating the Gulf of Mexico and Atlantic coasts. In contrast, microsatellite data only distinguished samples north and south of Cape Hatteras, and suggested considerable gene flow among native samples with clear evidence of isolation by distance. Both cytb and microsatellite data sets indicated that the northern invaders (North/Baltic Seas) originated from north of Cape Hatteras, with cytb data pointing to Delaware and north. Microsatellite data indicated a source for the southern invaders (Black, Caspian and Mediterranean Seas) to be south of Cape Hatteras, while cytb data narrowed the source location to the Gulf of Mexico region. Both cytb and microsatellite data sets suggested that the southern invasion was associated with genetic bottlenecks while evidence was equivocal for the northern invasion. By increasing the native range spatial sampling, our dataset was able to sufficiently characterize patterns and levels of genetic differentiation in the native range of M. leidyi and identify likely biogeographic boundaries, allowing for the most complete characterization of M. leidyi’s invasion histories and most realistic estimates of its source region(s) to date.

Mouse lemurs (genus Microcebus) are nocturnal primates endemic to the island of Madagascar. Until recently, they were classified as two species, one from eastern and one from western Madagascar. Previously published analyses of morphometric and mitochondrial DNA data show strong support for the recognition of more than eight species, however. Here, we test the eight-species hypothesis with DNA data derived from four independently segregating nuclear loci. We find many areas of congruence between the mitochondrial and nuclear data, but incomplete lineage sorting and low mutation rates limit the phylogenetic resolution of the nuclear data. Even so, the nuclear loci unanimously find evidence for three deeply diverged lineages within the mouse lemur radiation: one that is congruent with the mtDNA "southern clade", another that is congruent with the mtDNA "northern clade", and one monospecific branch comprised of the species Microcebus ravelobensis. The latter result in particular emphasizes the need for careful biological study of this species.