Phylogeography Unplugged: Comparative Surveys in the Genomic Era

In March 2012, the authors met at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, USA, to discuss approaches and cooperative ventures in Indo-Pacific phylogeography. The group emerged with a series of findings: (1) Marine population structure is complex, but single locus mtDNA studies continue to provide powerful first assessment of phylogeographic patterns. (2) These patterns gain greater significance/power when resolved in a diversity of taxa. New analytical tools are emerging to address these analyses with multi-taxon approaches. (3) Genome-wide analyses are warranted if selection is indicated by surveys of standard markers. Such indicators can include discordance between genetic loci, or between genetic loci and morphology. Phylogeographic information provides a valuable context for studies of selection and adaptation. (4) Phylogeographic inferences are greatly enhanced by an understanding of the biology and ecology of study organisms. (5) Thorough, range-wide sampling of taxa is the foundation for robust phylogeographic inference. (6) Congruent geographic and taxonomic sampling by the Indo- Pacific community of scientists would facilitate better comparative analyses. The group concluded that at this stage of technology and software development, judicious rather than wholesale application of genomics appears to be the most robust course for marine phylogeographic studies. Therefore, our group intends to affirm the value of traditional (“unplugged”) approaches, such as those based on mtDNA sequencing and microsatellites, along with essential field studies, in an era with increasing emphasis on genomic approaches

Phylogeography Unplugged: Comparative Surveys in the Genomic Era

In March 2012, the authors met at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, USA, to discuss approaches and cooperative ventures in Indo-Pacific phylogeography. The group emerged with a series of findings: (1) Marine population structure is complex, but single locus mtDNA studies continue to provide powerful first assessment of phylogeographic patterns. (2) These patterns gain greater significance/power when resolved in a diversity of taxa. New analytical tools are emerging to address these analyses with multi-taxon approaches. (3) Genome-wide analyses are warranted if selection is indicated by surveys of standard markers. Such indicators can include discordance between genetic loci, or between genetic loci and morphology. Phylogeographic information provides a valuable context for studies of selection and adaptation. (4) Phylogeographic inferences are greatly enhanced by an understanding of the biology and ecology of study organisms. (5) Thorough, range-wide sampling of taxa is the foundation for robust phylogeographic inference. (6) Congruent geographic and taxonomic sampling by the Indo-Pacific community of scientists would facilitate better comparative analyses. The group concluded that at this stage of technology and software development, judicious rather than wholesale application of genomics appears to be the most robust course for marine phylogeographic studies. Therefore, our group intends to affirm the value of traditional ( unplugged ) approaches, such as those based on mtDNA sequencing and microsatellites, along with essential field studies, in an era with increasing emphasis on genomic approaches

Peripatric speciation drives diversification and distributional pattern of reef hermit crabs (Decapoda: Diogenidae: Calcinus)

The diversity on coral reefs has long captivated observers. We examine the mechanisms of speciation, role of ecology in speciation, and patterns of species distribution in a typical reef‐associated clade—the diverse and colorful Calcinus hermit crabs—to address the origin of tropical marine diversity. We sequenced COI, 16S, and H3 gene regions for ∼90% of 56 putative species, including nine undescribed, “cryptic” taxa, and mapped their distributions. Speciation in Calcinus is largely peripatric at remote locations. Allopatric species pairs are younger than sympatric ones, and molecular clock analyses suggest that \u3e2 million years are needed for secondary sympatry. Substantial niche conservatism is evident within clades, as well as a few major ecological shifts between sister species. Color patterns follow species boundaries and evolve rapidly, suggesting a role in species recognition. Most species prefer and several are restricted to oceanic areas, suggesting great dispersal abilities and giving rise to an ocean-centric diversity pattern. Calcinus diversity patterns are atypical in that the diversity peaks in the west-central oceanic Pacific rather than in the Indo-Malayan diversity center. Calcinus speciation patterns do not match well-worn models put forth to explain the origin of Indo-West Pacific diversity, but underscore the complexity of marine diversification

Identification of a Ciliopagurus strigatus (Herbst, 1804) species-complex, with description of a new species from French Polynesia (Crustacea, Decapoda, Anomura, Diogenidae)

Four hermit crabs of the genus Ciliopagurus are recognized as a complex of species named the “strigatus complex”. They are found in the low intertidal or shallow waters of the Indo-West Pacific. Ciliopagurus strigatus (Herbst, 1804) is characterized by striped legs and chelae with alternate yellow and red transverse colour bands. It is commonly found on reef habitats and is reported from the Red Sea to French Polynesia. Ciliopagurus tricolor Forest, 1995 is reported with certainty from East Africa to Réunion Island, C. vakovako Poupin, 2001 is endemic to the Marquesas Islands, and C. galzini n. sp. is described as a new species from specimens collected in the Tuamotus. Within the 17 extant species of the genius Ciliopagurus, these four species are distinct by the aspect of the ocular acicle with 3-5 terminal spines instead of usually 1 or 2 in the other species, a few morphometric characters, and by their vertical distribution, from intertidal to about 20 m, whereas all the other species are usually collected deeper. The species of the strigatus complex are morphologically very similar and can be separated with confidence only by their coloration. All of them have similar colour patterns of transverse bands on the cheliped and walking legs, but each species can be easily recognized by the distinct colour and/or disposition of these bands. The appraisal of these colour differences as valuable specific indicators is confirmed by phylogenetic analysis of mitochondrial and nuclear DNA sequences

Peripatric speciation drives diversification and distributional pattern of reef Hermit Crabs (Decapoda: Diogenidae: Calcinus)

The diversity on coral reefs has long captivated observers. We examine the mechanisms of speciation, role of ecology in speciation, and patterns of species distribution in a typical reef-associated clade-the diverse and colorful Calcinus hermit crabs-to address the origin of tropical marine diversity. We sequenced COI, 16S, and H3 gene regions for similar to 90% of 56 putative species, including nine undescribed, "cryptic" taxa, and mapped their distributions. Speciation in Calcinus is largely peripatric at remote locations. Allopatric species pairs are younger than sympatric ones, and molecular clock analyses suggest that > 2 million years are needed for secondary sympatry. Substantial niche conservatism is evident within clades, as well as a few major ecological shifts between sister species. Color patterns follow species boundaries and evolve rapidly, suggesting a role in species recognition. Most species prefer and several are restricted to oceanic areas, suggesting great dispersal abilities and giving rise to an ocean-centric diversity pattern. Calcinus diversity patterns are atypical in that the diversity peaks in the west-central oceanic Pacific rather than in the Indo-Malayan "diversity center." Calcinus speciation patterns do not match well-worn models put forth to explain the origin of Indo-West Pacific diversity, but underscore the complexity of marine diversification

Three new species of pagurid hermit crabs (Decapoda: Anomura: Paguroidea) from the Northern Mariana Islands, Micronesia

Komai, Tomoyuki, Miller, Allison K., Malay, Maria Celia D. (2022): Three new species of pagurid hermit crabs (Decapoda: Anomura: Paguroidea) from the Northern Mariana Islands, Micronesia. Zootaxa 5099 (5): 563-585, DOI: 10.11646/zootaxa.5099.5.

FIGURE 8. Nematopagurus marianicus n in Three new species of pagurid hermit crabs (Decapoda: Anomura: Paguroidea) from the Northern Mariana Islands, Micronesia

FIGURE 8. Nematopagurus marianicus n. sp., holotype, SIO-BIC C14523, male (sl 2.8 mm). A, right pereopod 2, lateral view; B, same, carpus, mesial view; C, same, dactylus and distal part of propodus, mesial view; D, left pereopod 3, lateral view; E, same, dactylus and distal part of propodus, mesial view.Published as part of Komai, Tomoyuki, Miller, Allison K. & Malay, Maria Celia D., 2022, Three new species of pagurid hermit crabs (Decapoda: Anomura: Paguroidea) from the Northern Mariana Islands, Micronesia, pp. 563-585 in Zootaxa 5099 (5) on page 575, DOI: 10.11646/zootaxa.5099.5.4, http://zenodo.org/record/611024

FIGURE 1. Catapagurus tenuilamina n in Three new species of pagurid hermit crabs (Decapoda: Anomura: Paguroidea) from the Northern Mariana Islands, Micronesia

FIGURE 1. Catapagurus tenuilamina n. sp., holotype, SIO-BIC C14512, male (sl 2.7 mm). A, shield and cephalic appendages, dorsal view; B, distal two peduncular articles and flagella of left antennule, lateral view; C, left maxilliped 3, lateral view; D, same, basis and ischium, ventral view; E, coxae of chelipeds, ventral view; F, dactylus, propodus and carpus of left pereopod 4, lateral view; G, coxae of pereopods 5 and thoracic sternite 8, ventral view; H, distal part of right sexual tube, crossing dorsal surface of anterior part of pleon; I, thoracic sternite 6, ventral view; J, telson, dorsal view.Published as part of Komai, Tomoyuki, Miller, Allison K. & Malay, Maria Celia D., 2022, Three new species of pagurid hermit crabs (Decapoda: Anomura: Paguroidea) from the Northern Mariana Islands, Micronesia, pp. 563-585 in Zootaxa 5099 (5) on page 566, DOI: 10.11646/zootaxa.5099.5.4, http://zenodo.org/record/611024

FIGURE 7. Nematopagurus marianicus n in Three new species of pagurid hermit crabs (Decapoda: Anomura: Paguroidea) from the Northern Mariana Islands, Micronesia

FIGURE 7. Nematopagurus marianicus n. sp., holotype, SIO-BIC C14523, male (sl 2.8 mm). A, left cheliped, mesial view; B, same, lateral view; C, same, chela, dorsal view (setae omitted); D, same, carpus, dorsal view.Published as part of Komai, Tomoyuki, Miller, Allison K. & Malay, Maria Celia D., 2022, Three new species of pagurid hermit crabs (Decapoda: Anomura: Paguroidea) from the Northern Mariana Islands, Micronesia, pp. 563-585 in Zootaxa 5099 (5) on page 574, DOI: 10.11646/zootaxa.5099.5.4, http://zenodo.org/record/611024

FIGURE 6. Nematopagurus marianicus n in Three new species of pagurid hermit crabs (Decapoda: Anomura: Paguroidea) from the Northern Mariana Islands, Micronesia

FIGURE 6. Nematopagurus marianicus n. sp., holotype, SIO-BIC C14523, male (sl 2.8 mm). A, right cheliped, mesial view; B, same, lateral view; C, same, chela, dorsal view (setae omitted); D, same, carpus, dorsal view (setae omitted).Published as part of Komai, Tomoyuki, Miller, Allison K. & Malay, Maria Celia D., 2022, Three new species of pagurid hermit crabs (Decapoda: Anomura: Paguroidea) from the Northern Mariana Islands, Micronesia, pp. 563-585 in Zootaxa 5099 (5) on page 573, DOI: 10.11646/zootaxa.5099.5.4, http://zenodo.org/record/611024