In 2017 an emergency field effort was undertaken in an attempt to prevent the extinction of the world's most endangered marine mammal, the vaquita Phocoena sinus. The rescue effort involved 90 experts from 9 countries and cost US$ 5 million. Following a long decline due to entanglement in legal gillnet fisheries, the vaquita population had fallen from more than 200 to fewer than 30 individuals from 2008 to 2016, due to entanglement in an illegal gillnet fishery that supplies swim bladders of the endangered totoaba Totoaba macdonaldi to Chinese black markets. An emergency ban of gillnets and increased enforcement failed to slow the decline, triggering an emergency effort to catch vaquitas and place them under protection in captivity. Two animals were targeted and captured using light gill nets; a juvenile was released 4 h later because it appeared stressed, and an adult female died of capture myopathy. The program was suspended because of the risk of additional mortalities to the population. The lack of success in capturing vaquitas for temporary protection emphasizes the need to improve our understanding of the effects of chase, capture, handling and enclosure on cetaceans, and to consider intervention before populations reach critically low levels, when there is sufficient time to use phased, precautionary approaches. Furthermore, conservation approaches focused on single species must be integrated into broader efforts to conserve ecosystems and involve the human communities that depend on them.
Introgression and hybridization are major impediments to genomic-based species delimitation because many implementations of the multispecies coalescent framework assume no gene flow among species. The sunfish genus Lepomis, one of the world’s most popular groups of freshwater sport fish, has a complicated taxonomic history. The results of ddRAD phylogenomic analyses do not provide support for the current taxonomy that recognizes two species, Lepomis megalotis and Lepomis peltastes, in the L. megalotis complex. Instead, evidence from phylogenomics and phenotype warrants recognizing six relatively ancient evolutionary lineages in the complex. The introgressed and hybridizing populations in the L. megalotis complex are localized and appear to be the result of secondary contact or rare hybridization events between nonsister species. Segregating admixed populations from our multispecies coalescent analyses identifies six species with moderate to high genealogical divergence, whereas including admixed populations drives all but one lineage below the species threshold of genealogical divergence. Segregation of admixed individuals also helps reveal phenotypic distinctiveness among the six species in morphological traits used by ichthyologists to discover and delimit species over the last two centuries. Our protocols allow for the identification and accommodation of hybridization and introgression in species delimitation. Genomic-based species delimitation validated with multiple lines of evidence provides a path towards the discovery of new biodiversity and resolving long-standing taxonomic problems.[ddRAD; genealogical divergence index; hybridization; integrative species delimitation; phylogeny; secondary contact; systematics; taxonomy.]
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